Amazon FBA vs Shopify: Which Should You Start With?

What Are You Actually Comparing?

The search "Amazon FBA vs Shopify" compares two things that sit at different levels. Fulfillment by Amazon is a service inside Amazon's marketplace: you list a product there, send your stock to Amazon's fulfilment centers, and Amazon stores it and ships each order. Amazon's own definition is one sentence.

A Shopify store is a storefront of your own. You pay a monthly plan, you bring the visitors, and you decide how orders are shipped. So the choice for a first product is narrower than the search suggests: rent a place inside Amazon's store, or open your own.

The two are also not mutually exclusive. Amazon's Multichannel Fulfillment (MCF) fulfils orders placed on your own website, and, in the US, Buy with Prime shows the Prime logo and delivery promise on a site you already run. Both reach a Shopify store through one app, Amazon MCF and Buy with Prime, which uses your existing Amazon inventory. Amazon describes it as a free Shopify app, and its listing says it is free to install and that additional charges may apply.

Going the other way, Shopify Marketplace Connect lists a Shopify catalogue on marketplaces including Amazon. That makes the order of operations the real question: which channel first, and when to add the second.

What Does It Cost to Start and to Stay Listed?

Neither route asks for much before the first sale, and the two subscriptions are within a dollar of each other. The table sets the fixed costs side by side; the three subsections explain what sits behind each column.

Amazon's Two Selling Plans

Amazon sells two plans, and after registering you can switch or cancel your selling plan at any time. In Amazon's US store, the Individual plan has no subscription and charges $0.99 for each item sold, and the Professional plan is $39.99 a month while you have active listings, with no per-item fee. You can use FBA with either.

The arithmetic between them is short, and it is ours rather than Amazon's: 40 sales on the Individual plan cost $39.60 in per-item fees, almost exactly the Professional subscription. Below about 40 sales a month Individual is the cheaper plan, and above it Professional is. That matches the threshold Amazon itself names, saying FBA "might be a more cost-effective choice if you sell 40 items or more per month with a Professional plan."

Two details matter more than the break-even. Amazon's advertising tools need a Professional account, so a seller who plans to advertise is choosing Professional whatever the volume. And Vacation mode does not pause it: Amazon confirms that the Professional fee is charged for the period an account spends in that mode.

What Amazon Gives New Sellers, and on What Conditions

Amazon advertises over $50,000 in automatic referral-fee waivers for a new-to-Amazon brand in its first year, and that headline sits behind conditions. As of October 2026 the programme, New Seller Incentives, is open to new sellers on the Professional plan, and its main benefits are these:

• Brand owner bonus. A $52,500 credit applied as a discount on referral fees — 10% on the first $50,000 of branded sales and 5% on the next $950,000 — for up to one year. It is for sellers whose first buyable listing dates from March 12, 2026 or later, who complete Amazon Brand Registry before listing or within six months after, and who are the first owner of the brand in Brand Registry.
• FBA credits. If your first FBA shipment is received within 90 days of listing: $100 off inbound shipping with Amazon's partnered carrier or a $200 fulfilment credit with Amazon Global Logistics, plus $400 in credits toward the inbound placement service fee.
• Fee exemptions. New sellers are exempt from the storage utilization surcharge, and new Professional sellers from the low-inventory-level fee, for the first 365 days after their first FBA inventory is received.
• Advertising credits. Up to $1,000 in promotional click credits for spending on Sponsored Products within 90 days of listing, scaled to that spend; unused click credits expire 30 days after they are applied.

Read these as a discount on a route you have already chosen, not as a reason to choose it. The largest item only exists for a registered brand, and each credit has an expiry.

Shopify's Side: Plan, Trial and What Stacks on Top

A Shopify store has no per-item fee and no choice between selling plans at the start. In the US, Shopify Basic is $39 a month billed monthly, or $29 a month billed yearly. As of October 2026 Shopify starts with a 3-day free trial that needs no credit card, and most plans then cost $1 a month for the first 3 months before standard pricing applies; the amount differs by country.

That sticker price is the floor of what a store costs, not the bill. Card processing comes off every order, and app subscriptions, a paid theme or a third-party payment provider each add a line of their own. We break that stack down in our catalogue of Shopify's disadvantages.

Basic is the entry plan, not the only one. What the higher plans change, and when an upgrade pays for itself, is covered in our Shopify pricing guide.

What Comes Off Every Sale?

Fixed fees decide little. What separates the two routes is what leaves with each order, and on Amazon that is two separate charges before any storage bill, plus $0.99 per item on the Individual plan and a $1.80 closing fee per item in Books, DVD, Music, Software & Computer/Video Games, Video Game Consoles and Video Game Accessories.

Amazon's Referral Fee

For every item sold, Amazon takes a referral fee: a percentage of the total sales price or a minimum amount, whichever is greater. The total sales price is what the buyer paid, including any delivery or gift-wrap charge, so the fee applies to the shipping you charge as well as to the item.

The percentage depends on the product's fee category, which Amazon warns may not be the category shoppers see in its store. On Amazon's US fee schedule as we counted it on October 10, 2026, 14 of the 38 category rows carry a flat 15%. A few rows show the spread:

• Home and Kitchen, Toys and Games, Sports and Outdoors: 15%
• Consumer Electronics and Computers: 8%
• Clothing and Accessories: 5% on a total sales price of $15 or less, 10% above $15 and up to $20, 17% above $20
• Beauty, Health and Personal Care, and Baby Products: 8% on items up to $10, 15% above that
• Amazon Device Accessories: 45%

A refund does not return the whole fee. When you refund a buyer for an order you have already been paid for, Amazon gives back the referral fee minus a refund administration fee, which is the lesser of $5.00 or 20% of that referral fee. On FBA returns it also states that it does not reimburse the applicable FBA fees.

The FBA Fulfilment Fee

The second charge is the FBA fulfilment fee, which Amazon defines as a per-unit fee to fulfil items to customers. It is set by the product's size tier, its weight and the price band it sells in, and it is charged when the buyer's order is shipped. It is also this route's shipping bill: the fee pays for packing and delivering each order, which a store of your own pays for separately.

Weight is not always what the scale says. For large standard items and bigger, Amazon uses the greater of the unit weight and the dimensional weight, which is the unit's volume (length × width × height) divided by 139. Small standard items are charged on unit weight.

To anchor the scale: for a small standard item priced between $10 and $50, Amazon's 2026 non-peak table lists $3.32–$3.96 per unit, from the lightest band of 2 oz or less to the heaviest of 14 to 16 oz, apparel excluded. Items priced under $10 get lower rates and items above $50 higher ones, and an item priced at exactly $10 or $50 falls in the $10–$50 band.

Those table values are not the full charge. Since April 17, 2026, Amazon adds a 3.5% fuel and logistics-related surcharge to FBA fulfilment fees in the US, and the fee tables do not include it.

Which FBA Fees Does a Quick Estimate Leave Out?

Amazon says the costs of FBA depend on the products you sell and the exact services you use, and that is where a first estimate goes wrong: it stops at the referral and fulfilment fees. The table lists the further charges we verified on Amazon's US pages on October 10, 2026.

It is the set we read, not a claim that the list is complete. Where a figure is missing, we read the rule but did not verify a rate card for this article.

Read the second column for the pattern. Storage, the utilization surcharge, the aged surcharge and removal all grow when stock sits, and the low-inventory fee appears when stock runs too thin. FBA is priced for inventory that turns at a steady pace, and a first product, whose sales rate nobody knows yet, is the hardest case to keep inside that band.

What a Sale Costs on Your Own Store

Your own store has no referral fee and no per-unit fulfilment fee from the platform. What comes off each order on Shopify Basic in the US is the card rate: 2.9% + 30¢ for standard online cards through Shopify Payments, per Shopify's pricing page. If you take payments through a third-party provider instead, Shopify adds a third-party transaction fee of 2% on Basic.

The honest counterweight is that the platform fee is not the whole cost of the sale. You pay to pack and ship every order, and you pay, in ads, content or time, for every visitor, because a new store has no shoppers of its own. On Amazon those two costs are folded into the fulfilment fee and the marketplace.

Which route leaves more from one unit depends on your price, weight and category, so it has to be run on your own numbers. We keep that calculation, with a calculator you can load your own product into, in the fee section of our Shopify and Amazon integration guide.

What Do You Commit When Stock Goes Into FBA?

On your own store, unsold stock is a box in a spare room. In FBA it is a line on a monthly invoice, and the line changes with the season and with how long the units have been there.

Capacity Limits and Storage Rates

How much you can send depends on the plan. Individual selling accounts have a capacity limit of 15 cubic feet, which Amazon says does not change and cannot be increased. New Professional accounts, meaning those active in FBA for less than 39 weeks, receive no capacity limit; after that the limit is influenced by the account's IPI score and by factors such as historical sales volume and forecasts.

The limit has teeth. If your stock on hand plus shipments on the way to Amazon exceeds it, you are blocked from creating new shipments.

Storage itself is charged monthly on the daily average volume your stock occupies. For standard-size products the base rate is $0.78 per cubic foot from January through September and $2.40 from October through December, so the months when a seller most wants deep stock are the months it costs most to hold.

The 181-Day Clock

The charge that turns a slow product into a loss is the one attached to age. Amazon's rule fits in one sentence.

The surcharge is assessed from an inventory snapshot on the 15th of each month and is charged in addition to the monthly storage fee. The ladder Amazon has applied since January 16, 2026 starts gently and then breaks: $0.50 per cubic foot for units aged 181–210 days, $5.45 at 271–300 days, and at 366–455 days $6.90 per cubic foot or $0.30 per unit, whichever is greater. The three bands below 271 days do not apply to clothing, shoes, bags, jewelry and watches.

Leaving is not free either. Amazon will return, dispose of or liquidate inventory for a per-item charge, set for removals by the unit's shipping weight, and a disposal order is typically processed in 14 business days, or 30 business days or more during the holiday season and removal peaks.

Arrival has its own risk. Amazon may refuse, return or repackage any product delivered with inadequate or non-compliant packaging or labelling, and inventory that arrives in non-compliant, unsafe packaging may be refused or disposed of at your expense, without reimbursement.

Where Stock Sits When You Sell on Shopify

Selling from your own store, the stock stays wherever you put it: at home, with a third-party logistics provider, or with a supplier who ships for you, which is the only one of these routes open to a seller who holds no stock at all. The price of that freedom is the work, because picking, packing and posting each order is yours or it is a 3PL's invoice; we compare those two costs in our 3PL vs in-house fulfillment guide.

When Does the Money Reach Your Bank?

A marketplace and a store pay you on different clocks, and for a first product bought with your own money the clock matters. Amazon says that, in general, it settles seller accounts every two weeks: it takes the beginning balance, adds sales, subtracts expenses, adjusts for refunds, and transfers the payment after withholding an amount in reserve.

Two more waits sit around that cycle. Funds from a delivered order are typically reserved for seven days, to give the customer time to inspect the purchase, and once Amazon initiates a payment it can take up to five business days for the funds to appear in your bank account.

On your own store with Shopify Payments in the US, payouts typically arrive within 3 to 5 business days after a customer's payment is captured. The minimum settlement time is 3 business days, and there is no minimum payout amount.

It is not instant on this side either. Shopify says settlement time is longer when you begin receiving payouts and can decrease as you reliably fulfil orders on time, and payments captured on Friday, Saturday and Sunday are grouped into one payout. A reserve exists here too: a temporary hold on a portion, in some cases the full amount, of transactions for a specified period.

The gap is wider than the payout line suggests, because FBA adds bills before the first sale. If you hold stock, you buy it on either route; with FBA you also ship it in, and the bills that follow do not wait for revenue: the inbound placement fee, where it applies, is charged 45 days after the shipment is received, and storage is charged monthly, typically between the 7th and the 15th of the following month.

Who Brings the Buyer, and Who Keeps Them?

Demand is the reason sellers start on Amazon, and the customer is the reason they open a store. Both arguments are true at once, which is why this is the section to read twice.

Amazon Brings the Shoppers and Sells You the Visibility

What you rent on Amazon is the shopper. An FBA offer is put in front of people already shopping in Amazon's store, with Prime delivery attached.

Being listed is not the same as being seen, and Amazon is direct about the next step: it recommends launching a Sponsored Products campaign first. These are cost-per-click ads that promote individual listings, with no monthly cost, so you pay only when a shopper clicks.

Amazon's ad tools require a Professional selling account, and Brand Stores, Sponsored Brands and display ads additionally require a brand enrolled in Amazon Brand Registry. Treat clicks as part of the launch budget, and size that budget against your own margin.

On Amazon, the Buyer Stays Amazon's

The limit that shapes a brand's long-term economics is in Amazon's Communication Guidelines. All communication between a seller and a buyer has to go through Amazon's Buyer-Seller Messaging service, and the policy closes the other doors explicitly.

• Who you may message: only buyers who contacted you first about a possible purchase, or who recently bought from you through Amazon's store.
• What you may say: in general, only what completes an order or answers a customer-service question. Marketing or promotional messaging, including coupons and offers of free products, is prohibited content.
• What you may keep: customer information you receive to fulfil an order may be used only for that, and must be deleted after the order has been processed.
• What you receive: for US orders, Amazon's Orders API returns the buyer's email only on orders fulfilled by the seller, to developers holding a restricted Direct-to-Consumer Shipping role, and not on FBA orders.

Breaking the policy can lead Amazon to block a message, restrict your ability to send proactive messages, or suspend or terminate selling privileges.

For a product bought once, none of this costs much. For a product that depends on the second and third order, it means winning each repeat sale inside the marketplace again.

On Your Own Store the List Is Yours, and So Is the Traffic Bill

On your own store the relationship runs the other way: the customer's email and order history sit in your store, and bringing them back is your decision. The cost is the mirror image of Amazon's strength, because a new store starts with no shoppers and every visitor has to be earned or bought; we set out that trade in full, owning an audience versus renting one, in our TikTok Shop vs Shopify comparison.

What Can Get You Shut Off?

A first product is one supplier order and one account. What can close that account, and how much warning you get, is part of the cost of each route. On Amazon there are two separate gates: getting in, and staying in.

Getting In: Registration, Approval and Prep

Registration comes first. To be eligible to sell on Amazon you must be resident in one of the countries Amazon lists, have a valid phone number and have an internationally chargeable credit card.

Then comes the product. Some categories and products require approval before listing, which Amazon says is to ensure products sold in its store are safe, authentic and meet regulations. Certain products cannot be listed at all, for legal, regulatory or policy reasons.

The order of operations matters more than the rule. Check a product's approval status in Seller Central's Add Products tool before you pay a supplier, because approval is Amazon's decision and unsellable stock is yours.

The same holds at the warehouse door: if Amazon accepts inventory that violates shipment requirements or differs from the shipping plan, you may be issued an inbound defect fee.

Staying In: Account Health and Fair Pricing

Once you are selling, Amazon measures the account continuously. All new sellers start with an Account Health Rating of 200, and over time the score reflects policy adherence and selling activities over the last 180 days.

A rating of 100 to 199 is labelled "At Risk", meaning the account is at risk of deactivation, and reaching the maximum number of repeat violations of a single policy within a 180-day period can put an account at immediate risk. Above all of that sits one clause.

A deactivated seller can view the issues that led to the deactivation and submit an appeal on the Account Health page. With FBA the stakes are concrete, because the stock is in Amazon's buildings while the appeal runs.

Price is policed too. Under its Fair Pricing Policy, Amazon regularly monitors prices, including shipping costs, and compares them with other prices available to its customers; a price significantly higher than recent prices offered on or off Amazon is one of the practices it names.

Amazon can then remove the Featured Offer, remove the offer, suspend the ship option, or in serious or repeated cases suspend or terminate selling privileges. If you later open your own store, the price you set there is, by that wording, one of the prices offered off Amazon.

The Shopify Mirror: Softer Process, Same Final Clause

Your own store is not beyond anyone's rules. Shopify's Acceptable Use Policy sets out how it intends to act toward merchants who build with its principles in mind: it says it will give notice, grant opportunities to self-remediate conflicts, default to enforcement at the product level and take account-level action as a last resort when appropriate. It also says that if you do not act in good faith, account-level action may be appropriate.

The Terms of Service are blunter.

So the difference is one of stated process, not of final power: both companies can end the account. What Shopify's Terms allow, and how that differs from a store with restricted access, is answered in our FAQ on whether Shopify can shut down your store.

Sales Tax and Country Limits

Two boundaries sit outside the fee tables. The first is sales tax. As a marketplace facilitator, Amazon calculates, collects, remits and refunds sales tax on third-party sellers' transactions destined for states where marketplace facilitator legislation is enacted, which shifts that duty from the seller to Amazon for those orders.

It does not close the subject: Amazon states that you remain responsible for identifying your tax obligations and for all taxes within them. On your own store there is no marketplace facilitator, so where you owe sales tax, registering, collecting and remitting are yours, which is the subject of our Shopify US sales tax guide.

The second boundary is country. Amazon's seller registration is limited to residents of the countries on its list, and every Amazon figure in this article is for its US store.

On the Shopify side the limit sits on the payment service: Shopify Payments is available only to businesses located in one of 40 supported countries, and a store outside them runs on a third-party provider and pays the third-party transaction fee. Check the list in our Shopify Payments guide before you plan around the Shopify Payments card rate.

Which Should You Start With?

The verdict table at the top answers by one profile at a time. This quiz answers by combination: where your stock is, how shoppers find the product, whether you already have people to sell to, how much the second order matters, and whether the margin survives Amazon's referral and fulfilment fees.

Two answers settle the route on their own, having no stock to send or no margin left after the fees, and the quiz says so; otherwise it weighs the rest. Every route ends in three steps.

The Bottom Line

The two subscriptions cost about the same, so the plan fee decides nothing. What decides is what each route asks of you after the first sale: Amazon asks for a share of every order, stock that keeps moving and a customer relationship you never own, while your own store asks you to find every buyer and ship every box. Neither is the safe choice for every product.

Frequently Asked Questions