Shopify vs. Amazon FBA (2025): Which Is Better for Selling Online?

When it comes to starting or scaling an online business, many entrepreneurs face the crucial decision of choosing the right platform to sell their products. The debate of Shopify vs Amazon FBA is one of the most popular comparisons among ecommerce sellers today. Both platforms offer unique advantages — from Shopify’s customizable ecommerce platform ideal for building your own brand to Amazon FBA’s fulfillment service that handles storage and shipping for you. In this article, we’ll explore the key differences between Shopify and Amazon FBA, including setup ease, fees, profitability, and target audience, to help beginners and seasoned sellers decide which option best fits their business goals.

Shopify vs Amazon FBA: Quick Stats (2025)

Before we dive deeper, here are some quick stats that show the scale and growth potential of both platforms in 2025.

Shopify Statistics (2025):

• Over 4 million active stores worldwide
• Average Shopify store earns $67,000 annually
• Shopify powers 22% of the top 1 million websites globally

Amazon FBA Statistics (2025):

• Amazon Marketplace has over 310 million active users
• Sellers using Amazon FBA grow sales 30% faster on average
• Over 200 million customers subscribe to Amazon Prime, and FBA sellers can deliver directly to this high-converting audience

Cost Comparisons:

• In 2025, Shopify’s Basic plan begins at a monthly cost of $39, making it accessible for new online sellers
• Average Amazon FBA referral fees range from 8% to 15% per sale
• Fulfillment fees for Amazon FBA average $3 to $5 per unit depending on size and weight

What is Shopify?

Shopify is a top ecommerce platform that allows users to build and manage their own online stores effortlessly. Unlike marketplaces, Shopify gives sellers complete control over their brand, website design, and customer experience. It offers a wide range of customizable templates, built-in payment processing, and powerful marketing tools that help entrepreneurs launch and grow their stores quickly.

Shopify is particularly popular among small to medium-sized businesses that want to build a unique online presence without relying on third-party marketplaces. With its user-friendly interface and scalable features, Shopify remains one of the best choices for those looking to start a branded online store.

What is Amazon FBA?

Amazon FBA (Fulfillment by Amazon) is a popular business model where sellers list their products on Amazon’s marketplace, and Amazon handles storage, packaging, and shipping on their behalf. This allows entrepreneurs to focus on sourcing and marketing their products without worrying about logistics.

Amazon FBA offers access to Amazon’s vast customer base and trusted fulfillment network, making it an attractive choice for those who want to leverage Amazon’s infrastructure. While Amazon manages order fulfillment, sellers must follow Amazon’s rules and pay associated fees. Understanding the Amazon FBA business model is essential for sellers deciding whether to use this service or opt for a self-hosted ecommerce platform like Shopify.

Differences Between Shopify and Amazon FBA

When comparing Shopify vs Amazon FBA, it’s important to understand the fundamental differences that set these two platforms apart. Shopify is a fully customizable ecommerce platform where you build and manage your own online store, giving you full control over branding, design, and customer experience. In contrast, Amazon FBA is a fulfillment service tied to Amazon’s massive marketplace, where your products are sold alongside millions of others, and Amazon handles storage, packaging, and shipping.

One major difference lies in customer ownership: with Shopify, you own your customer data and can build direct relationships, whereas Amazon controls customer information on its platform. Additionally, Shopify requires sellers to manage marketing and drive traffic to their stores, while Amazon’s marketplace provides built-in exposure to millions of shoppers.

Understanding these key differences helps sellers decide whether they want the independence and branding opportunities of Shopify or the convenience and vast audience of Amazon FBA.

Setup and Ease of Use

When deciding between Shopify and Amazon FBA, ease of setup is a critical factor, especially for beginners. Shopify offers a user-friendly interface designed to help anyone, even those with no technical background, build a fully functional online store quickly. Its drag-and-drop store builder, customizable themes, and integrated payment options simplify the setup process, making it accessible to small business owners and entrepreneurs.

On the other hand, Amazon FBA involves setting up a seller account on Amazon’s platform and sending inventory to Amazon’s fulfillment centers. While Amazon takes care of storage and shipping, the initial setup can be more complex, including navigating Amazon’s seller policies, listing optimization, and inventory management. Additionally, new sellers may find Amazon’s strict rules and fees challenging to manage.

If you want a simple way to launch and manage your own store, Shopify tends to be more user-friendly, but Amazon FBA appeals to sellers comfortable using a large platform and learning its nuances.

Costs, Fees & Subscriptions

Understanding the costs involved is essential when comparing Shopify vs Amazon FBA fees to determine which platform fits your budget and business model. Shopify charges a monthly subscription fee that varies depending on the plan you choose, ranging from basic plans for startups to advanced plans for larger businesses. Shopify charges transaction fees on top of the subscription, except when using Shopify Payments. You’ll also need to budget for additional expenses like premium themes, apps, and marketing costs.

Amazon FBA’s fee structure is different. While there is no monthly subscription fee to use Amazon’s marketplace, sellers must pay referral fees on each sale, which vary by product category, and fulfillment fees for storage, packing, and shipping. These fees can add up, especially for products with low profit margins or seasonal inventory. Holding inventory over an extended time can result in extra long-term storage charges for sellers.

Both platforms have distinct fee models, and your choice will depend on your product type, sales volume, and how much control you want over your expenses. Comparing selling costs on Amazon vs Shopify can help you make a more informed decision tailored to your business needs.

Shopify vs Amazon FBA Comparison Table (2025)

Here’s a side-by-side breakdown to help you quickly evaluate both platforms.

Feature	Shopify	Amazon FBA
Business Model	Own your ecommerce site	Sell through Amazon marketplace
Setup Difficulty	Easy drag-and-drop store builder	Moderate; involves listing, shipping inventory
Monthly Fees	Starts at $39/month + fees	No base fee, but 8–15% referral + fulfillment fees
Fulfillment	Self-managed or third-party logistics	Handled entirely by Amazon
Customer Ownership	You own customer data & relationships	Amazon controls the customer experience
Marketing	You manage ads, SEO, email, etc.	Access to Amazon’s massive search traffic
Profit Margin	Potentially higher, depending on strategy	Lower, but with high volume potential
Shipping Speed	Varies by fulfillment choice	Fast, Prime-eligible shipping
Branding Control	Full control over brand & design	Limited; products shown under Amazon branding
Best For	Sellers who want full ownership & branding	Sellers who want faster scaling with less overhead

Profitability Comparison

When evaluating Shopify vs Amazon FBA profit margin, profitability largely depends on your business model, product pricing, and operational costs. Shopify allows sellers to keep a larger portion of their sales revenue since they control pricing, marketing, and customer relationships. While Shopify has fixed monthly fees and transaction costs, the ability to build a unique brand and retain customer data can drive higher long-term profits.

In contrast, Amazon FBA offers the advantage of immediate access to a massive customer base, which can boost sales volume quickly. However, the fees associated with Amazon’s fulfillment service — including referral, storage, and shipping fees — can significantly reduce profit margins, especially for low-priced items. Additionally, competition on Amazon is fierce, often leading to price wars that further shrink margins.

Which platform yields higher profits—Shopify or Amazon FBA—largely depends on your product category, pricing tactics, and cost efficiency. Sellers focused on brand building and long-term customer loyalty often find Shopify more profitable, while those seeking quick scale and large sales volume may benefit from Amazon FBA despite tighter margins.

Fulfillment and Shipping

One of the biggest differences in the Shopify vs Amazon fulfillment debate lies in how orders are processed and shipped to customers. With Shopify, sellers are responsible for managing their own fulfillment or partnering with third-party logistics (3PL) providers. This gives sellers flexibility and control over packaging, shipping options, and delivery experience, but it also means more hands-on management and potential operational challenges.

Amazon FBA, on the other hand, offers a fully managed fulfillment service where Amazon stores your inventory in their warehouses, picks, packs, and ships orders on your behalf. This makes order fulfillment hassle-free and fast, benefiting from Amazon’s extensive logistics network and Prime shipping options. However, this convenience comes at a cost — sellers must pay fulfillment fees and adhere to Amazon’s shipping standards.

Choosing between Shopify’s self-managed fulfillment and Amazon’s streamlined FBA service depends on your business model, budget, and how much control you want over the shipping experience. For sellers prioritizing convenience and fast delivery, Amazon FBA is often the preferred choice, while those wanting complete control over branding and customer service may lean towards Shopify fulfillment.

Target Audience and Reach

Comparing Shopify and Amazon requires recognizing how their customer audiences differ in size and scope. Shopify empowers sellers to build their own branded online stores, attracting customers through marketing efforts like SEO, social media, and paid ads. This means you own your customer relationships and data, allowing for personalized communication and long-term loyalty.

In comparison, Amazon FBA grants sellers instant entry to a vast audience of millions on one of the world’s biggest online platforms. This built-in audience offers high visibility but comes with intense competition and limited control over customer interactions. On Amazon, your brand is often overshadowed by the marketplace itself, which can make building direct customer loyalty more challenging.

The choice between the two hinges on your specific business objectives. If you want to establish a unique brand and cultivate a dedicated customer base, Shopify is the better option. But if you’re looking for volume sales and immediate market access, Amazon FBA’s expansive reach is hard to beat.

Can You Use Shopify and Amazon FBA Together?

Yes, many sellers successfully combine Shopify and Amazon FBA together to maximize their sales channels and business growth. Leveraging both Shopify and Amazon FBA lets you benefit from Shopify’s customizable platform to create your brand and control the customer experience, along with Amazon FBA’s robust fulfillment services and large customer base.

This approach enables you to sell through Shopify while Amazon FBA takes care of storage, packing, and shipping, so you can maintain your branded storefront without the hassle of fulfillment. Additionally, selling on both platforms diversifies your revenue streams and reduces dependency on a single marketplace.

However, managing two platforms requires careful inventory synchronization and marketing strategies to avoid stockouts or conflicting pricing. Many sellers use integration tools and apps that connect Shopify with Amazon FBA to streamline operations.

In summary, combining Shopify with Amazon FBA is a popular and effective strategy for sellers aiming to grow their business and reach a wider audience.

Shopify vs Amazon FBA: Pros and Cons

Aspect	Shopify	Amazon FBA
Pros	Full control over branding and customer experience Highly customizable ecommerce platform Own your customer data for targeted marketing Flexible payment options and integrations	Access to Amazon’s massive customer base Amazon handles storage, packing, and shipping Fast shipping with Amazon Prime benefits Simplified fulfillment process
Cons	Responsible for managing fulfillment and shipping Requires effort to drive traffic and marketing Monthly subscription and transaction fees Steeper learning curve for store customization	Fees can reduce profit margins Less control over branding and customer relationships Must comply with Amazon’s rules and policies High competition within the marketplace

This comparison highlights that Shopify is ideal for sellers who want brand ownership and control, while Amazon FBA suits those looking for convenience and wide reach despite higher fees and less control.

Frequently Asked Questions (FAQ)

Q1: Which is better for beginners, Shopify or Amazon FBA?

For beginners, Shopify offers a straightforward way to build a custom online store with complete control, while Amazon FBA provides access to a huge marketplace but requires understanding Amazon’s rules and fees.

Q2: How do Shopify and Amazon FBA fees compare?

While Shopify charges both a monthly subscription and transaction fees, Amazon FBA’s costs include referral, storage, and fulfillment fees. Your total expenses depend on sales volume and product type.

Q3: Can I sell the same products on both Shopify and Amazon FBA?

Yes, many sellers leverage both platforms to broaden their audience. You can showcase your products on Shopify while relying on Amazon FBA for fulfillment.

Q4: Do I need to handle shipping if I use Amazon FBA?

No, Amazon manages the storage, packing, and delivery processes. Shopify sellers usually manage their own fulfillment or use third-party logistics.

Q5: Which platform offers better profitability?

Profitability is influenced by your business model, product pricing, and associated fees. Shopify allows more control over margins, while Amazon FBA offers higher sales volume but with added fees.

Conclusion

Deciding between Shopify and Amazon FBA ultimately comes down to your business goals, available resources, and priorities. If you want full control over your online store, branding, and customer relationships, and are willing to invest time in marketing and fulfillment, Shopify is the ideal ecommerce platform for building a sustainable, scalable business.

On the flip side, Amazon FBA offers easy access to a massive marketplace and handles fulfillment for you, making it ideal for those who value convenience and fast shipping over full control of their brand.

For many sellers, a hybrid approach using both Shopify and Amazon FBA together offers the best of both worlds: customizable branding with Shopify and streamlined logistics plus massive reach with Amazon.

Consider your product type, budget, and long-term vision to decide which platform aligns best with your entrepreneurial goals. Whichever you choose, understanding the Shopify vs Amazon FBA comparison will help you make an informed, strategic decision to grow your ecommerce business successfully.