7 Best ERPs for Shopify and Amazon Inventory Sync in 2026

You have one unit left. A shopper buys it on Shopify at 9:02, and four minutes later someone buys the same unit on Amazon, because Amazon still thinks you have it. One order now gets cancelled, and on Amazon that cancellation counts against you.

The best ERP for Shopify and Amazon inventory sync prevents that by running both channels off a stock count that updates on every order. Below are seven tools, what each one does for you and what it costs.

We're Prim.io, one of the seven, and we process more than 3.1 million orders every month. Each entry uses the same checks and published facts, so the choice stays with you.

TL;DR

• Selling everything from your own warehouse? Any tool here with native Shopify and Amazon connectors can run both channels from one stock pool.
• Using FBA as well? Your stock sits in two places, so watch how each tool tracks units in Amazon's warehouses.
• NetSuite sells its connectors separately. Its Shopify and Amazon connectors are an add-on, on top of a yearly subscription and setup fee.
• A sync app can carry a one-location store. With stock in one place and no wholesale, Shopify Marketplace Connect can be enough.
• Prim.io Pro costs €540 a month. It's the plan for multi-channel retailers on Amazon and Shopify, billed annually, excluding VAT, plus onboarding.

How We Compared ERPs for Shopify and Amazon Inventory Sync

We ran every tool through the same five checks, starting with vendor pages and then, when a vendor stays quiet, named third-party sources.

• Native Shopify and Amazon connectors built by the vendor, with no third tool in between.
• One shared stock count that both channels read from.
• How the tool tracks FBA units sitting in Amazon's warehouses.
• Whether accounting lives in the same system, or in a second tool you pay for.
• What it costs, and the effort before live orders flow.

One Stock Pool or Two? How FBA Changes the Setup

Your setup decides what you need from a tool. FBM (Fulfilled by Merchant) means you store and ship Amazon orders yourself, while FBA (Fulfilment by Amazon) means you send stock to Amazon's warehouses and Amazon ships it.

If everything is FBM, life is simple: every unit sits on your shelf, and one shared stock pool works exactly as promised.

Many brands run a split instead, with FBA shipping Amazon orders and your warehouse shipping Shopify orders, meaning two stock pools and two reorder points.

The third route, Amazon Multi-Channel Fulfilment (MCF), lets FBA stock ship your Shopify orders too. Its fees rose on 15 January 2026, and apparel and footwear can't ship in unbranded packaging.

As you read the list, ask whether each tool can show your FBA units as their own location, next to your warehouse.

Quick Comparison of Shopify and Amazon Inventory Tools

At a glance, this is what each tool connects, where your accounting lives and what you'll pay.

1. Prim.io

Prim.io is an ERP for brand owners and retailers, with orders, stock, purchasing, warehouse and finance in one place, as our full ERP feature set shows.

Shopify, Amazon FBA and Amazon FBM each have a native connector on our integrations page, among 50+ channels. A sale on either channel lands in the same stock count, and your warehouse and accounts see it together.

Running two warehouses, or selling bundles? Multi-warehouse and bills of materials come built in, so a bundle sale takes each item off the count. Teams go live in about six weeks on average.

On price, Plus is €180 a month, Pro €540 and Enterprise €1,710, billed annually without VAT, as Prim.io plans and pricing shows. Plus and Pro carry a €1,300 one-time onboarding fee, and full accounting is a €100-a-month add-on in selected countries.

Best for:

• Brands juggling stock in multiple locations, or wholesale orders alongside online sales.
• Teams running FBA and FBM side by side who want both in one count.

Watch out for:

• One warehouse and no wholesale? A full ERP may be more system than you need right now.
• We don't publish a stock sync interval yet, so ask us for the number in your demo.

2. NetSuite

NetSuite is Oracle's ERP, with full accounting at its core, so if your finance team already lives there, keeping stock in it saves a second system.

Shopify and Amazon don't come in the box, though. They connect through the NetSuite Connector, which NetSuite sells as "an add-on module," and its channel list covers Shopify, Amazon Seller Central and Amazon Multi-Channel Fulfilment.

FBA isn't on that list by name. If a good share of your stock sits with Amazon, expect some extra setup to see those units next to your own warehouse.

Prices aren't on the site. NetSuite quotes a yearly subscription based on modules and users, plus a one-time setup fee, with the connector on top.

Best for:

• Larger companies whose finance already runs on NetSuite.
• Teams with an IT department or partner who can own the connector.

Watch out for:

• Get the subscription, setup fee and connector in one quote, so the total isn't a surprise.

3. Brightpearl

Brightpearl, part of Sage since 2022, is a "retail operating system" that runs orders, stock, warehouses and accounting, general ledger included, for retailers and wholesalers.

Its blog describes Brightpearl's Shopify and Amazon integrations as "native Plug & Play integrations," covering stock, prices and orders across several Shopify stores. Handy if you run a store per region.

On the Amazon side, Brightpearl can map its warehouses to Amazon's fulfilment centres for Multi-Channel Fulfilment, so your FBA stock can ship Shopify orders as well.

Best for:

• Retailers and wholesalers who want stock and accounting in one retail-focused system.
• Brands running several Shopify stores that also sell on Amazon.

Watch out for:

• Pricing is by quote only, so you'll need a sales call before you can compare.
• Reviewers on Software Advice mention extra charges for some channel and accounting integrations, so check which ones your quote covers.

4. Cin7

Cin7 calls itself an inventory management system, sometimes "ERP Lite." It's built around stock, purchasing, and multi-channel orders, and it connects to the accounting software you already use.

Shopify is its home turf, and the Cin7 Shopify integration promises "Native two-way sync with Shopify" across several stores, plus Amazon, wholesale, and POS.

Amazon is where you'll want to slow down. Cin7's help center says FBA needs its own add-on, new Amazon orders are pulled hourly, and returns don't restock on their own.

An hour is fine on a quiet Tuesday. During a sale, it's long enough for your last unit to sell twice.

Cin7 Core starts at $349 a month on Standard, with Pro at $599 and Advanced at $1,199, according to Capterra's 2026 listing.

Best for:

• Inventory-first teams running several Shopify stores.
• Brands that sell wholesale and through POS as well as online.

Watch out for:

• Your books stay in a separate accounting tool, so you'll run and pay for two systems.
• Stock only reaches Amazon when an optional setting is on, so switch it on before your first busy day.

5. Odoo

Odoo is a general-purpose ERP built from apps you switch on as needed, accounting included, with plenty of room if you like shaping software around your process.

For Amazon, the Odoo Amazon Connector lets you "Synchronise your Amazon orders and manage deliveries in Odoo" across nine marketplaces. It brings orders in and confirms shipping, but the page doesn't mention pushing stock to Amazon.

Shopify runs through a module published by Odoo IN and listed as a third-party app that Odoo supports. Orders sync every 10 minutes, and stock coming back from Shopify is fetched manually.

Need FBA, or stock sent to Amazon? Emipro's connector on Odoo's app store covers FBA and FBM for $615.10, plus €99 a month after a free period.

Odoo's own plans run $24.90 per user a month on Standard and $37.40 on Custom, according to The CFO Club's July 2026 breakdown.

Best for:

• Teams who enjoy configuring an ERP and adding modules.
• Businesses already running other Odoo apps.

Watch out for:

• A 10-minute order sync leaves a window where both channels can sell your last unit.
• Full Amazon coverage may mean a paid third-party module on top of your plan.

6. Zoho Inventory

Zoho Inventory is a stock and order app, lighter than a full ERP, and it pairs with Zoho Books for accounting.

Its Amazon integration page calls it "FBA ready," so you can send stock to FBA and fulfill orders from other channels through it. After any order, "the stock-on-hand details of that item will be pushed to all channels automatically."

Shopify connects per store, and your plan sets the limit, from one store on Standard up to five on Premium and Enterprise.

Pricing is refreshingly public: free for 50 orders a month, then $29 to $249 a month per organization, billed annually.

Best for:

• Small sellers already using other Zoho apps.
• Growing stores that want FBA support at a low, published price.

Watch out for:

• Accounting lives in Zoho Books, a separate app, so add its cost to your budget.
• Zoho mentions "scheduled syncs" without an interval, so time a test order first.

7. Shopify Marketplace Connect

The Shopify Marketplace Connect app is Shopify's own way to sell on Amazon, eBay, Walmart, and Target Plus, all from your Shopify admin.

For orders you ship yourself, the Marketplace Connect fulfilment guide says "Inventory counts are updated in Shopify and on Amazon." In other words, Shopify holds the count, and Amazon follows it.

Your first 50 synced orders each month are free, then you pay 1% per order, capped at $99, so even a busy store's bill has a ceiling.

Best for:

• Stores with stock in one location and no wholesale.
• Sellers testing Amazon as a new channel.

Watch out for:

• Shopify publishes no sync interval, so run a test order before a big sale.
• The app treats Shopify as the single source of truth, so stock held anywhere else stays invisible to it.

Why Shopify and Amazon Stock Drifts Apart

Shopify and Amazon each keep their own count, so without a live link, every sale leaves the other channel wrong.

Amazon staff set out the cancellation target in Amazon's pre-fulfilment cancel rate guidance, a US Seller Central forum post: "The target for this metric will remain under 2.5% and will look at a period of 7 days." FBA orders don't count, but every oversold FBM order does.

Amazon staff guidance for UK sellers warns that a high rate "can start putting your seller-fulfilled listings at risk if it keeps happening."

Real-Time Sync vs. Batch Updates

Batch updates send stock changes on a schedule, and between runs both channels show the old count. Published intervals vary, from Odoo's 10-minute Shopify sync to Cin7's hourly Amazon check.

Amazon adds its own delay, too. Its developer documentation says bulk feed processing "can take up to eight hours," so batch-heavy tools can lag even when their own side is instant.

Quiet days hide all of this. Prime Day won't.

Before you sign, ask how long an Amazon order takes to change your Shopify stock, and whether the tool updates Amazon per SKU or in bulk. Until you know, hold a small buffer.

How to Sync Shopify Inventory to Amazon With an ERP

• Connect Shopify. Link your store so orders and stock flow into the ERP, using our Shopify store setup guide.
• Connect Amazon. Add your seller account and choose FBA, FBM or both, then connect an Amazon marketplace in Prim.io.
• Match SKUs. Map each Shopify SKU (the code for one product variant) to its Amazon listing.
• Decide your stock pools. Run one shared pool if everything ships from your warehouse, or keep FBA as its own location, with a small buffer per channel.
• Set reorder points per pool. At 10 Amazon sales a day and a 20-day FBA restock, reorder at 200 units plus buffer. Shopify: at 4 sales a day and a 10-day lead time, reorder at 40.
• Test with slow sellers. Run a few low-volume SKUs for a week, then switch to your best sellers.
• Check cancel rate weekly. Watch it in Amazon Account Health and trace each stock-related cancellation to its SKU.

Review buffers and reorder points monthly, with extra care on FBA, since Amazon has tightened restock limits in 2026.

What Does a Shopify-Amazon ERP Cost?

Total cost has four parts: the subscription, implementation, any paid connectors, and your team's time. Each tool's published price sits in its entry above, and our breakdown of how ERP costs compare covers the implementation and training side.

Staff time is the part buyers forget, so count the hours spent fixing stock by hand.

Key Takeaways

• One shared count works when stock sits in one place. With FBA, your tool needs to track two pools.
• Sync speed varies. Published intervals run from 10 minutes to an hour, before Amazon's own feed delays.
• Check where accounting lives. NetSuite, Brightpearl and Odoo include it, Prim.io offers it as an add-on, and Cin7 and Zoho Inventory lean on another tool.

Shopify and Amazon Inventory Sync FAQ

How Does Shopify Connect to Amazon?

Through Shopify's Marketplace Connect app, from your Shopify admin. Brands with FBA stock, several warehouses, or wholesale may need an ERP on top.

Can I Use FBA Stock for Shopify Orders?

Yes, through Amazon Multi-Channel Fulfilment. Amazon ships the Shopify order from your FBA stock for a per-unit fee.

Pick Your Stock Setup First, Then the Tool

The right tool depends on where your stock lives. If everything ships from your own warehouse, any option here with native connectors can run one shared count.

With FBA in the mix, look hardest at how each tool tracks units held at Amazon, then put the sync-speed question to your shortlist.

Want to see it with your own channels? Open a free Prim.io demo account with no credit card needed.

Prefer a guided tour? Book a 30-minute walkthrough with our team