Amazon FBA vs Shopify for CPG Brands: Which Is Better?

1. Amazon FBA vs Shopify: What’s the Difference for CPG Brands?

The main difference between Amazon FBA and Shopify is where customers buy your products and how orders are fulfilled.

Amazon is a marketplace with existing shoppers. Shopify lets you sell through your own website.

Selling CPG Products Through Amazon FBA

With Amazon FBA (Fulfillment by Amazon), you list your products on Amazon and send inventory to its fulfillment centers. When a customer places an order, Amazon handles storage, packing, shipping, customer service, and returns for FBA orders.

For example, if you sell a skincare moisturizer, shoppers may find it when they search Amazon for a moisturizer. You can also use Amazon PPC advertising to get your product in front of relevant shoppers.

You’ll compete with similar brands and pay Amazon selling and FBA fees.

Selling CPG Products Through Shopify

Shopify allows you to sell products directly to customers through your own branded website.

Customers buy the moisturizer on your website, where you control the product page, offers, and customer messages.

Unlike Amazon FBA, Shopify doesn’t automatically handle physical order fulfillment. You’ll need to ship orders yourself or work with a third-party logistics provider (3PL).

You will need to promote your store, often by paying for Google, Facebook, Instagram, or TikTok ads to introduce your brand and generate orders. SEO can bring visitors from Google over time, and email can bring past buyers back.

For CPG brands, the key difference is that Amazon already has people shopping for products like yours. Shopify gives you your own store, but you need a plan to get people there and turn visits into orders.

2. Amazon FBA vs Shopify: Side-by-Side Comparison

Amazon helps you reach people already searching for products like yours. Shopify lets you follow up with customers who agree to receive messages, such as a reminder to reorder their skincare or supplements.

However, neither platform is automatically more profitable. Look at what you spend on product costs, shipping, fees, and ads before deciding which option leaves more profit.

3. Amazon FBA vs Shopify Fees for CPG Brands

Amazon charges referral and fulfillment fees. Shopify charges store and payment fees, plus any apps you use.

Amazon FBA Selling and Fulfillment Costs

If you’re selling CPG products through Amazon FBA, the main expenses include:

• Seller account fee: Amazon’s Professional selling plan costs $39.99 per month.
• Referral fees: Amazon charges a percentage of each sale based on the product category.
• FBA fulfillment fees: Covers picking, packing, shipping, and handling customer orders. The fee depends primarily on product size and weight.
• Inventory storage fees: Charged monthly based on the space your products occupy in Amazon’s fulfillment centers.
• Inbound shipping and placement fees: Costs associated with transporting and distributing inventory to Amazon’s fulfillment network.
• Amazon PPC advertising: Additional spending on Sponsored Products, Sponsored Brands, or other advertising campaigns.

Amazon referral fees vary across CPG categories:

These rates apply to the relevant Amazon US categories. Other categories, minimum referral fees, and additional charges may apply.

A small skincare serum usually costs less to fulfill than a heavy detergent bottle. Product size and weight matter when pricing CPG products.

Shopify Selling and Fulfillment Costs

Shopify doesn’t charge Amazon-style marketplace referral fees, but CPG brands still have several operating expenses.

The main costs include:

• Shopify subscription: The Basic plan costs $39 per month when billed monthly or $29 per month when billed annually.
• Payment processing: Standard US online card rates on the Basic plan start at 2.9% + $0.30 per transaction through Shopify Payments.
• Order fulfillment: Shipping, packaging, and warehouse handling costs, whether you fulfill orders yourself or use a 3PL.
• Apps and integrations: Additional charges for subscriptions, product bundles, loyalty programs, or other services.
• Customer acquisition: The money you spend on Google, Facebook, Instagram, or TikTok ads to get orders.

If you use a third-party payment provider instead of Shopify Payments, additional transaction fees may apply.

Which Platform Has Lower Selling Fees?

Shopify generally charges less in platform and payment fees per sale, but you still pay to pack and ship orders. If people don’t already know your brand, you’ll likely also need to pay for ads to build awareness and generate sales.

Amazon charges referral and fulfillment fees, but provides access to an established marketplace where customers are already searching for products.

For CPG brands, lower platform fees don’t necessarily mean higher profits. Instead, check how much money you keep from each order after products, shipping, ads, and other selling costs.

4. Which Is More Profitable for CPG Brands: Amazon FBA or Shopify?

Profitability depends on more than Amazon’s referral fees or Shopify’s payment processing charges. For CPG brands, contribution profit is the amount left after paying for the product, shipping, ads, and selling fees.

Example 1: Selling a $19.99 Skincare Product

Suppose you sell a facial moisturizer for $19.99, with a landed product cost of $4 per unit.

These are illustrative figures, not actual quotes or guaranteed results. Amazon’s 15% referral fee for beauty products above $10 and Shopify Basic’s standard 2.9% + $0.30 US payment rate are based on published pricing. Fulfillment, storage, and advertising costs are assumptions.

Here, Amazon leaves $1.08 more per order because the assumed shipping and ad costs are lower.

But if shoppers already find that Shopify store through Google without an ad, or previous customers keep reordering, the brand may spend less on advertising per sale. That could change the result.

Example 2: Selling a Three-Pack Instead of a Single Product

CPG brands often sell products individually and in multipacks. With a multipack, you can sell and ship several units in one order instead of paying to win separate orders.

Suppose the same skincare brand introduces a three-pack priced at $49.99.

Using illustrative costs of $12 for the products, $7.50 for Shopify fulfillment and shipping, $1.75 for payment processing, and $8 for advertising, the Shopify store would generate $20.74 in contribution profit per order.

Under a separate Amazon FBA scenario with $12 in product costs, $7.50 in referral fees, $5.25 in fulfillment fees, $0.80 in inbound and storage costs, and $8 in advertising, the contribution profit would be $16.44.

In this example, Shopify performs better for the multipack. However, actual results depend on the bundle’s dimensions, weight, selling price, customer acquisition costs, and fulfillment arrangements.

First-Order Profit vs. Repeat-Purchase Profit

For regularly purchased products like supplements and skincare, first-order profit is only part of the picture.

For example, you might spend $6 on ads to get a first-time Shopify customer. If they reorder after an email reminder, you may not need to pay for another ad to get that second sale.

Amazon also supports recurring orders through Subscribe & Save, although seller-funded discounts can reduce the profit earned on each subscription order.

This is why CPG brands should measure both contribution profit per order and profit from repeat purchases.

The calculations above exclude fixed business overhead, returns, taxes, and other costs not specifically listed. Before deciding which channel is more profitable, compare your actual product-level costs and advertising performance rather than relying on platform fees alone.

5. Customer Acquisition: Amazon PPC vs Shopify Advertising

Getting new customers usually costs money. On Amazon, you pay to appear where people are shopping; on Shopify, you often pay to introduce people to your brand and bring them to your store.

Finding Customers Through Amazon PPC

Amazon attracts shoppers who are already searching for products. For example, someone searching for “vitamin C serum” or “protein powder” may be ready to compare products and make a purchase.

You can pay to show your products to these shoppers with Amazon ads such as:

• Sponsored Products: Promote individual products in search results and on product detail pages.
• Sponsored Brands: Display brand-focused ads featuring products, videos, or a link to your Amazon Brand Store.
• Sponsored Display: Reach relevant audiences through product and audience targeting.

Higher product rankings can bring orders from unpaid search results without paying for every click.

Finding Customers Through Shopify Advertising

A new Shopify store won’t automatically be shown to the shoppers searching on Amazon. Most new brands need to run ads so people learn about their products, visit the website, and place orders.

Ways to bring shoppers to your Shopify store include:

• Meta Ads: Pay for Facebook and Instagram ads that introduce your products and link to your store.
• Google Ads: Pay to appear when someone searches Google for products like yours.
• TikTok Ads: Run short product-demonstration videos as ads to introduce your brand.
• SEO and Content Marketing: Write useful pages and articles that can appear in unpaid Google searches.
• Influencer Marketing: Pay or collaborate with creators who can demonstrate your products to their followers.

Comparing Customer Acquisition Costs

Amazon and Shopify use different metrics to measure advertising performance.

For example, spending $500 on Amazon advertising to generate $2,000 in ad-attributed sales produces a 25% ACoS.

On Shopify, spending $500 to acquire 50 new customers gives an advertising-only acquisition cost of $10 per customer. A complete CAC calculation should also include other relevant acquisition expenses.

These figures aren’t directly comparable. ACoS measures advertising costs against revenue, while CAC measures the cost of acquiring a customer.

For each channel, check what you spend to get an order, how much profit remains after its costs, and whether that customer comes back to buy again.

6. Repeat Purchases: Amazon Subscribe & Save vs Shopify Subscriptions

Repeat purchases matter for CPG brands because buyers regularly reorder vitamins, skincare, pet food, and household essentials.

Both support recurring orders, but offer different options for discounts, emails, changes, and cancellations.

How Amazon Subscribe & Save Works

Amazon Subscribe & Save lets customers schedule deliveries of eligible products, such as every two weeks or monthly.

For example, a customer buying a 30-day supply of vitamins can subscribe to receive another bottle every month without placing a new order manually.

For eligible products:

• Amazon automatically enrolls qualifying FBA products in Subscribe & Save.
• Sellers can offer an additional 5% or 10% discount on recurring orders.
• Amazon funds a 5% discount when customers receive five or more eligible subscription items in one delivery.
• Amazon handles recurring order fulfillment through FBA.

Eligibility depends on factors including Brand Registry status, product category, sales performance, and inventory availability.

How Shopify Subscriptions Work

Shopify allows CPG brands to offer recurring purchases through the Shopify Subscriptions app or supported third-party subscription apps.

Brands can create subscription plans with different delivery frequencies and discounts.

For example, a skincare brand could offer its $25 moisturizer for $22.50 with automatic delivery every 30 days.

With Shopify subscriptions, brands can:

• Offer weekly, monthly, or other recurring delivery schedules.
• Set their own subscription discounts and pricing.
• Allow customers to skip, pause, or cancel upcoming orders.
• Send subscription reminders and manage customer communication.
• Track active subscriptions, cancellations, and recurring orders.

Shopify lets you email subscribers who opt in, such as when it’s time to reorder.

Which Is Better for CPG Repeat Purchases?

Amazon Subscribe & Save is useful for generating repeat orders from marketplace customers, particularly for products customers already purchase regularly.

Shopify offers greater control over customer retention, including subscription offers, loyalty programs, and personalized email campaigns.

For CPG brands selling through both channels, check how many shoppers subscribe, how many order again, how many cancel, and how much money remains after discounts and delivery.

7. Inventory Management and Fulfillment for CPG Brands

CPG brands need to plan stock carefully. Supplements and food may expire, while popular skincare and pet products can sell out if you reorder too late.

Amazon FBA handles order fulfillment for marketplace sales, while Shopify gives brands flexibility to manage their own inventory and choose fulfillment partners.

How Amazon FBA Handles CPG Inventory

With Amazon FBA, you send your products to Amazon’s fulfillment centers, where they’re stored until customers place orders.

Amazon handles picking, packing, shipping, and customer returns. Sellers can monitor stock levels, track inbound shipments, and manage inventory through Seller Central.

However, CPG brands still need to manage:

• Inventory replenishment: Sending new stock before popular products sell out.
• Storage costs: Avoiding excess inventory that remains in fulfillment centers for extended periods.
• Product shelf life: Making sure expiration-dated products meet Amazon’s requirements.
• Inventory forecasting: Using recent daily or monthly sales and supplier lead times to decide when to reorder.

For example, a supplement brand selling 300 bottles monthly needs to account for manufacturing and inbound shipping times when planning replenishment.

How Shopify Orders Are Fulfilled

Shopify doesn’t require brands to use a particular fulfillment provider. You can choose how and where your products are stored and shipped.

The main options are:

• Self-fulfillment: Store products at your own facility and pack and ship customer orders.
• Third-party logistics (3PL): Use a warehouse that stores inventory and handles order fulfillment.
• Multiple fulfillment locations: Distribute inventory across warehouses or retail locations and manage orders through Shopify.

Can Shopify Orders Be Fulfilled Using Amazon FBA Inventory?

Yes. Amazon Multi-Channel Fulfillment (MCF) allows brands to use inventory stored in Amazon’s fulfillment centers to fulfill orders placed through Shopify.

For example, a skincare brand selling on both Amazon and Shopify can use the same Amazon inventory to fulfill orders from both channels.

Amazon’s MCF and Buy with Prime app connects with Shopify, so stock counts stay updated, Shopify orders can be sent to Amazon for shipping, and customers receive tracking details.

MCF has its own fulfillment fees, which differ from standard Amazon FBA fees.

For CPG brands selling through both channels, using MCF may mean you don’t need one warehouse for Amazon and another for Shopify. Track combined sales so inventory doesn’t run out.

8. CPG Product Restrictions, Expiration Dates and Compliance

CPG brands selling supplements, skincare, food, pet products, or household essentials must meet applicable product safety, labeling, and regulatory requirements.

Amazon and Shopify have different selling requirements, which can affect whether a product can be listed, how it is stored, and how orders are fulfilled.

Amazon FBA Requirements for CPG Products

Amazon has category-specific requirements, and certain CPG products need additional documentation or approval before they can be sold.

Here are some common requirements by product category:

For example, a supplement brand may need to provide testing and manufacturing documentation before Amazon approves its products.

Expiration Dates and Storage Requirements

Products such as vitamins, snacks, and creams may expire, so check how much shelf life remains before sending inventory to a warehouse.

Amazon requires expiration-dated FBA inventory to meet its applicable shelf-life rules. Products that are too close to expiration may be refused or removed from sale.

Some temperature-sensitive products, including refrigerated and frozen foods, are also unsuitable for standard Amazon FBA fulfillment.

With Shopify, brands can choose warehouses and fulfillment providers that meet their products’ storage requirements. However, they remain responsible for maintaining product quality and complying with applicable laws.

Does Shopify Have Fewer Product Restrictions?

On Shopify, you choose which compliant products to list and who will store and ship them. However, this doesn’t mean every CPG product can be sold without restrictions.

Products must still comply with FDA, FTC, and other applicable regulations. Shopify Payments and certain sales channels may also restrict regulated products or require additional verification.

For CPG brands, compliance should be checked before choosing a sales channel, particularly when selling supplements, food, cosmetics, or products containing potentially hazardous ingredients.

9. Branding, Customer Data and Customer Relationships

Branding on Amazon vs Shopify

Amazon allows registered brands to show shoppers more detail about their products using:

• A+ Content: Add detailed product images, videos, comparisons, and brand information to product listings.
• Amazon Brand Store: Create a branded storefront displaying your products and collections.
• Brand Story: Introduce your brand and help customers discover related products.

However, Amazon controls the overall shopping experience, including the product detail page layout and checkout process.

With Shopify, you have greater control over your website’s design, product pages, checkout experience, and promotions.

For example, a skincare brand can create dedicated landing pages for different skin concerns, introduce its ingredients, and recommend complementary products throughout its website.

Customer Data and Purchase Insights

Amazon provides registered brands with valuable information through Amazon Brand Analytics, including:

• Search Query Performance
• Repeat Purchase Behavior
• Customer demographics
• Market Basket Analysis
• Customer Loyalty Analytics

These reports help CPG brands understand which products customers purchase together, how often they reorder, and which search terms contribute to sales.

However, Amazon doesn’t provide unrestricted access to individual buyer information for independent marketing.

Shopify provides direct access to customer profiles, order histories, and purchase behavior through the store’s admin dashboard. Brands can group buyers, such as repeat customers or people who haven’t ordered recently, and send relevant messages to those who have opted in.

Building Long-Term Customer Relationships

Shopify allows CPG brands to communicate with customers who have agreed to receive marketing messages.

For example, a supplement brand can send replenishment reminders, introduce new flavors, or recommend related products based on previous purchases.

Amazon restricts promotional communication with marketplace buyers. Sellers cannot use Amazon customer information or package inserts to redirect shoppers to their own websites for purchases.

For CPG brands, Shopify lets you email customers who opt in, send refill reminders, and recommend related products, while Amazon provides useful marketplace insights and tools for building brand recognition among Amazon shoppers.

10. Product Pricing, Multipacks and Bundles

Many CPG products are relatively inexpensive, so a few extra dollars in delivery or advertising costs can eat up much of the profit. Items such as snacks, skincare products, and household cleaners can become less profitable when fulfillment and advertising costs take up a large portion of each sale.

Offering multipacks and bundles can help brands increase their average order value and spread shipping costs across more products.

Pricing and Multipacks on Amazon FBA

On Amazon, CPG brands can sell individual products or offer multipacks, such as a three-pack of protein bars or two bottles of shampoo.

For example, a skincare brand might sell one cleanser for $12.99 and a three-pack for $32.99. The multipack gives customers a lower price per bottle while allowing the brand to generate more revenue from one order.

However, Amazon has specific product bundling policies. For consumable categories, including grocery, pet care, baby products, health, and beauty, bundles must meet Amazon’s manufacturer and brand ownership requirements.

Multipacks containing identical products are treated differently from bundles containing complementary products.

Product Bundles and Pricing on Shopify

Shopify gives CPG brands more flexibility to create product combinations and promotional offers.

Using Shopify’s free Bundles app, brands can offer:

• Multipacks: Three bottles of the same skincare cleanser.
• Product bundles: A cleanser, moisturizer, and facial serum sold together.
• Promotional sets: A selection of products offered at a discounted combined price.

Brands can also use compatible third-party apps for more customized bundles, such as allowing customers to choose their preferred skincare products or snack flavors.

Which Platform Is Better for CPG Bundles?

On Amazon, multipacks can appeal to shoppers who want several weeks’ worth of products such as shampoo, snacks, or pet treats.

Shopify offers more flexibility for introducing complementary products, gift sets, and customized product combinations.

Before pricing bundles, add up product, discount, packing, delivery, and ad costs. A larger order only helps if the extra revenue covers the additional product, packaging, and delivery costs.

11. Which Platform Is Better for Different CPG Categories?

A lightweight $30 serum, a $12 snack pack, and a heavy detergent bottle won’t have the same costs on Amazon or Shopify. Compare price, shipping weight, and how often people reorder before choosing where to sell.

What Should CPG Brands Consider?

For example, a lightweight facial serum priced at $29.99 may work well through Amazon FBA because of its relatively small shipping size and established category demand.

However, a heavy household cleaning product priced at $12.99 may struggle with FBA fulfillment costs. Selling it through Shopify as part of a larger bundle could be more profitable, depending on shipping costs and customer acquisition expenses.

Run the numbers for each product rather than assuming every skincare, supplement, or pet-care product belongs on the same platform. Two similar products can have different margins because of pricing, packaging, ads, and repeat orders.

12. Should CPG Brands Choose Amazon, Shopify or Both?

When Should CPG Brands Prioritize Amazon FBA?

Amazon FBA may be the better starting point if:

• Shoppers are already searching Amazon for the type of product you sell.
• Your selling price leaves enough profit after Amazon’s selling fees, FBA fees, and ads.
• You want to reach customers already comparing products in your category.
• Your website has few visitors and you haven’t yet built a regular base of direct customers.
• Your products are suitable for Amazon’s storage and fulfillment requirements.

For example, a supplement brand with a competitively priced magnesium product may benefit from reaching customers already searching for magnesium supplements on Amazon.

However, strong competition and advertising costs can make launching difficult without sufficient margins.

When Should CPG Brands Prioritize Shopify?

Shopify may make more sense if:

• You already have an audience through social media, retail, or other marketing channels.
• Your products benefit from customized bundles, subscriptions, or larger orders.
• You want greater control over customer communication and retention.
• Your Google or social ads bring sales at a cost you can afford, or shoppers already find you without ads.
• You want to sell personalized sets or let customers choose products for a routine.

For example, a skincare brand selling complete skincare routines may find Shopify useful for offering personalized product sets and encouraging repeat purchases.

When Does Selling on Both Make Sense?

For established CPG brands, selling through both Amazon and Shopify can reach customers who prefer different ways of shopping.

Amazon can reach marketplace shoppers searching for individual products, while Shopify can support direct purchases, subscriptions, and customized product collections.

However, managing both channels requires careful inventory planning, consistent branding, and separate profitability tracking.

Brands already selling through retail stores or wholesale distributors should also consider existing pricing agreements and channel relationships before expanding.

Our recommendation: Start where customers are most likely to buy and your prices leave enough profit after product, shipping, and advertising costs. Once that channel performs consistently, consider adding the second rather than splitting a limited advertising budget and inventory across both from the beginning.

13. How to Build an Amazon and Shopify Sales Strategy for Your CPG Brand

If you decide to sell through both Amazon and Shopify, decide which products each store will sell, who will ship the orders, and how much you can afford to spend on ads.

Step 1. Choose the Right Products for Each Channel

Check which products have enough margin for Amazon fees and which could sell well as bundles on your website.

For example, a skincare brand might sell individual cleansers and moisturizers on Amazon while offering complete skincare routines and customized sets through Shopify.

You don’t need to launch your entire catalog on both channels immediately.

Step 2. Calculate Profit Margins

Calculate the expected contribution profit for each product after accounting for product costs, selling fees, fulfillment, and advertising.

Compare individual products, multipacks, and subscriptions separately. Prioritize products that still make money after all costs, not just the products with the most orders.

Step 3. Plan Inventory and Fulfillment

Decide whether to maintain separate inventory for each channel or use a shared fulfillment solution such as Amazon Multi-Channel Fulfillment.

Track sales, stock, and supplier lead times to avoid running out.

Step 4. Create a Marketing Plan for Each Channel

On Amazon, focus on keyword research, listing optimization, product reviews, and PPC campaigns.

For Shopify, budget for Google, Facebook, Instagram, or TikTok ads to introduce products and get orders. Work on SEO so buyers can also find you through Google, and use email and subscriptions to encourage repeat sales.

Step 5. Monitor Performance and Adjust

Track sales, contribution margins, advertising expenses, and repeat-purchase rates separately for each channel.

Here’s a simple 90-day plan for adding another sales channel:

After 90 days, spend more on the products and ads that leave the most profit after costs.