Key Takeaways
- Amazon brings the shoppers, your site keeps them. Amazon has buyers already searching for your category. A Shopify site has no traffic until you pay for it, but you own the customer relationship.
- Compare margin per order, not fees. Amazon charges referral and fulfillment fees. Your own site charges you in advertising, payment processing and shipping. Either can win depending on price, size and repeat rate.
- Most manufacturers should start on Amazon. It is where product searches already happen, and it tests demand before you build a direct-to-consumer engine.
- Run both with one price. A cheaper price on your own site can cost you the Amazon Buy Box and anger retail partners.
- One inventory pool makes both work. A single warehouse or fulfillment setup feeding Amazon and Shopify keeps stock accurate and costs down.
For most manufacturers going direct for the first time, Amazon is the better first channel because shoppers are already searching there and you pay only when you sell. Your own Shopify site is the better second channel, because you own the customer data and repeat orders carry no marketplace fee. Mature brands run both, with one retail price and one inventory pool.
This article is for manufacturers choosing where to sell direct first. If you are still deciding whether to go direct at all, start with our pillar guide, Selling on Amazon as a Manufacturer. We run Amazon and Shopify side by side for brands, so what follows is how we think about the choice in practice.
Amazon vs Shopify: what is the real difference for a manufacturer?
Amazon is a marketplace. You rent space on the busiest product search engine in the US, follow its rules and pay a share of each sale. Shopify is software for running your own store. You own the storefront and the customer list, and you are responsible for every visitor who arrives.
| Amazon (Seller Central) | Your own Shopify site | |
|---|---|---|
| Where shoppers come from | Amazon search, already buying | Your ads, search engines, email, social and word of mouth |
| Main costs per order | Referral fee, fulfillment fees if you use FBA, advertising | Advertising to bring visitors, payment processing, shipping, apps |
| Who owns the customer | Amazon. You see orders, not a marketing relationship | You. Emails, repeat purchase and lifetime value are yours |
| Control of the page | Inside Amazon's templates and rules | Full control of design, bundles, content and offers |
| Trust at first visit | High. Shoppers know how Amazon returns and delivery work | Has to be earned by your brand and your site |
| Speed to first sale | Fast once listings are live and in stock | Slow without an existing audience |
| Main risk | Resellers, price wars, account and policy issues | Paying too much to acquire each customer |
Who finds you on each channel?
On Amazon, the shopper already wants the product
People go to Amazon to buy. Someone searching "brake pads for a 2019 F-150" or "stainless steel hose clamps" has a need and a card ready. Your job is to be on the first page with a listing that answers their question fast. That is why Amazon works well for manufacturers of replacement parts, tools, supplies and consumables: the demand is already there, and the channel just needs you to show up properly.
On your own site, you have to bring them
A new Shopify store gets almost no visitors on day one. Traffic comes from paid ads on Google, Meta or TikTok, from organic search over time, from email and from people who already know your name. For manufacturers with a well-known brand among dealers or professionals, branded search can bring real traffic early. For everyone else, the site grows as the brand grows, often fed by the awareness Amazon and social channels create.
TikTok Shop and social commerce
Social channels create demand rather than capture it. What we see is that TikTok Shop, Meta and Google traffic tends to lift branded searches on Amazon too. The channels feed each other. If your product demonstrates well on video, read our TikTok Shop guide for brands.
What does it cost to acquire a customer on Amazon vs Shopify?
On Amazon you pay a referral fee on every sale, a percentage of the price that runs between 8% and 15% in most categories. Advertising is optional in theory and necessary in practice for a new brand. The upside is that you pay for clicks from shoppers who are already searching for what you sell.
On Shopify there is no referral fee, but there is also no free traffic. Your cost to acquire a customer is your ad spend divided by the new customers it brings. On a first order, that is often higher than the Amazon fee plus Amazon advertising for the same product. The site wins on the second, third and tenth order, when the customer comes back through email or directly and you pay nothing to reach them.
So the honest answer is: Amazon is usually cheaper for the first sale, and your own site is usually cheaper for repeat sales. Which matters more depends on how often your customers reorder.
Which channel is more profitable per order?
Work out contribution margin per order on each channel: the price, minus product cost, minus every channel cost, before overhead. Here is the structure we use, with example numbers for a 40 dollar product so you can see how the math flows. These are for illustration only; use your own fees and costs.
| Per order (example) | Amazon with FBA | Shopify, first order | Shopify, repeat order |
|---|---|---|---|
| Price | 40.00 | 40.00 | 40.00 |
| Product cost | 12.00 | 12.00 | 12.00 |
| Marketplace referral fee (15%) | 6.00 | 0 | 0 |
| Fulfillment and shipping | 7.00 | 9.00 | 9.00 |
| Payment processing | 0 (inside referral fee) | 1.50 | 1.50 |
| Advertising per order | 6.00 | 15.00 | 1.00 |
| Contribution per order | 9.00 | 2.50 | 16.50 |
The pattern holds more often than not: Amazon beats a new site on the first order, and a site with a loyal customer base beats Amazon on repeat orders. Heavy or oversized products can flip the Amazon column, because fulfillment fees rise with size and weight. For a line-by-line version of the Amazon side, see how to calculate true Amazon profit margin.
What does each channel need operationally?
Amazon
- Amazon Brand Registry, which needs a registered or pending trademark
- Listings with strong titles, images and A+ content (see our listing optimization hub)
- Inventory sent to Fulfillment by Amazon (FBA), or your own shipping that meets Amazon's standards
- Advertising managed daily, not monthly (our PPC hub explains how)
- A plan for resellers and pricing, including a MAP policy
Shopify
- A site built to convert: product pages, reviews, fast checkout and clear shipping and return terms
- A traffic plan: paid social, paid search, search engine content and email
- Email and text flows for welcome, abandoned cart and reorder
- Parcel fulfillment, either in house or through a third-party logistics (3PL) warehouse
- Customer service for questions Amazon would normally absorb
The Shopify list is longer because you are building the store, the traffic and the service. That is the trade for owning the customer.
Not sure which channel should come first for your products? Our Growth Diagnostic is a full audit across Amazon, your own website, TikTok Shop and your other marketplaces, with a 90-day roadmap. It models margin per order on each channel with your real costs and recommends the order to build them in. The cost is credited to your first month if we work together. Start with a conversation.
Should a manufacturer start with Amazon, Shopify or both?
Here is the sequencing we recommend for most manufacturers, and the cases where it changes.
- Clean up and control Amazon first. Your products are probably on Amazon already through resellers. Enroll in Brand Registry, fix the listings, set your MAP policy and start selling direct through Seller Central. Amazon captures the demand that already exists.
- Launch a simple Shopify site alongside it. Even a small site gives dealers, professionals and loyal customers a place to buy direct, and it gives you a home for content, warranty registration and email capture.
- Grow the site once repeat buyers show up. When you see customers reorder, invest in email, subscriptions and paid acquisition on your own site, where repeat orders earn more.
- Add other marketplaces when the first two are stable. Walmart Marketplace and TikTok Shop come next for most brands. See our multi-marketplace strategy.
When Shopify should come first
- Your product is customized, configured or quoted, which Amazon handles poorly.
- You have a strong existing audience, such as a dealer network, trade following or email list.
- Your retail agreements restrict marketplace sales but allow your own site.
- Your product is expensive to ship and return, and Amazon's fees would erase the margin.
When Amazon should be the only direct channel for now
- You do not have the team or budget to drive traffic to a site.
- Your products are replacement parts or supplies that customers find by searching a part number.
How do you run Amazon and Shopify together without problems?
Keep one price
Amazon compares your Amazon price with prices it finds elsewhere, including your own site. If your site is noticeably cheaper, Amazon can remove the Buy Box from your listing, which cuts sales sharply. A cheaper direct price also undercuts your retail partners. Hold the same retail price on both, and use bundles, free shipping thresholds or loyalty perks on your site to reward direct buyers instead of discounts.
Use one inventory pool
Splitting stock between channels by hand leads to stockouts on one and dead stock on the other. Keep one pool in a warehouse that ships Shopify orders and replenishes FBA, or use Amazon Multi-Channel Fulfillment (MCF) to ship Shopify orders from your FBA inventory. We run our own 3PL in Kansas City so our clients can do this from one place.
Do not expect Amazon to cannibalize your site
Brands often worry Amazon will steal their website sales. In practice, many shoppers were going to buy on Amazon anyway. If you are not there, a reseller or a competitor takes the sale. What you can control is making sure the shopper who prefers your site finds a reason to buy there. For how we compared these channels in an earlier piece, see Amazon FBA vs Shopify.
Frequently Asked Questions
Is Amazon or Shopify better for a manufacturer?
For most manufacturers Amazon is the better first channel, because shoppers are already searching there and you pay mainly when you sell. Shopify is better once you have repeat customers, because you own the relationship and repeat orders carry no marketplace fee. Most established brands run both.
Which is more profitable, Amazon or Shopify?
Amazon is often more profitable on a first order because the traffic is already there. Your own site is often more profitable on repeat orders because you do not pay referral fees or much advertising to reach an existing customer. Heavy or oversized products can change the math, so model each product.
Can I sell the same products on Amazon and my own website?
Yes, and most brands do. Keep the retail price the same on both, because a lower price on your site can cost you the Amazon Buy Box and upset retail partners. Use bundles or perks on your site instead of discounts.
Can Amazon fulfill my Shopify orders?
Yes. Amazon Multi-Channel Fulfillment (MCF) ships orders from other channels using your FBA inventory. A 3PL that also replenishes FBA is another way to run both channels from one inventory pool.
Do manufacturers need Amazon Brand Registry to sell on Amazon?
You can sell without it, but you should not. Brand Registry, which needs a registered or pending trademark, gives you authority over your product pages, access to A+ content and a Brand Store, and tools to report counterfeits and listing abuse.