Ecommerce

ERP

Inventory Management

Ecommerce ERP Integration: Connecting Shopify, BigCommerce and Amazon to Your ERP

Sherman Hsieh

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Last updated: October 9, 2026 · Independent guide · We do not sell rankings or coverage.

Ecommerce ERP integration is the set of automated data flows that moves orders, customers and payouts from Shopify, BigCommerce and Amazon into your ERP, and sends items, available inventory, prices and fulfillment status back out to each channel. You can build it with a native connector from your ERP vendor, an iPaaS platform, a packaged third-party connector or custom API code. The pattern you pick matters less than deciding, field by field, which system owns each piece of data and how you will catch the records that fail to sync.

The eight stages of ecommerce ERP integration

1. Set the system of record for every data object (items, stock, prices, customers, orders, payouts).
2. Sync items and listings so every channel SKU maps to one ERP item.
3. Publish available inventory from the ERP to each channel, net of allocations and buffers.
4. Publish prices from ERP price lists, including B2B and customer-specific pricing.
5. Import orders and match customers into ERP sales orders with correct tax, shipping and payment terms.
6. Send fulfillment and tracking back to the channel that took the order.
7. Process returns and refunds as ERP credit documents tied to the original order.
8. Reconcile payouts and settlements so fees, refunds and deposits land in the general ledger.

Stage 1: Set the system of record for each data object

The IT lead owns this decision, with sign-off from finance and ecommerce. The output is a mapping document that names the owning system, sync direction, trigger (event or schedule) and conflict rule for each field.

A common split is that the ERP is the authoritative source for SKUs, pricing and inventory, while the storefront governs web-specific content. Customers are created online and sync to the ERP, which supplies credit limits and negotiated pricing at checkout (NetSuite, March 10, 2026; NetSuite sells ERP and commerce software). Our guide to ERP data integration covers the wider single-source-of-truth design.

What goes wrong: two systems both allowed to edit the same field, so a price changed in Shopify is silently overwritten on the next sync.

Stage 2: Sync items and listings

Merchandising usually owns this stage. Every channel SKU and variant must map to exactly one ERP item, including kits and bundles. An order line that does not map must stop in an exception queue rather than post as a miscellaneous charge.

On Amazon, FBA inventory sits in Amazon’s network, so treat it as a separate ERP location. Acumatica, for example, says its Amazon connector syncs listings, inventory and orders with Seller Central and supports both FBA and merchant-fulfilled workflows (Acumatica, no date shown).

Stage 3: Publish available inventory to each channel

Operations owns the rule for what quantity each channel sees. Publishing raw on-hand quantity causes overselling, because it ignores stock already promised to open orders.

Illustration (constructed numbers): your ERP shows 120 units on hand at the main warehouse. Open B2B sales orders have 30 units allocated, and you hold a 5-unit buffer against sync lag. You publish 85 units to Shopify and BigCommerce.

API limits cap how often you can push. Shopify’s GraphQL Admin API allows 100 cost points per second on standard plans, 200 on Advanced, 1,000 on Shopify Plus and 2,000 for Commerce Components (Shopify, no date shown). BigCommerce allows 150 requests per 30 seconds on Standard and Plus plans and 450 on Pro, and all apps on a store share that quota (BigCommerce, no date shown). Amazon’s FBA inventory summary call is limited to 2 requests per second (Amazon SP-API, September 9, 2026).

Stage 4: Publish prices from the ERP

Pricing or sales operations owns this stage. For B2C brands it is usually one list price. For distributors selling B2B online, it includes customer groups and contract prices, which is where connector depth varies most.

Microsoft says the Business Central Shopify connector can use selected customer price groups and discounts to set the prices exported to Shopify, and can define prices for catalogs linked to B2B companies (Microsoft Learn, October 20, 2025). Acumatica says its BigCommerce connector supports customer-specific pricing and keeps customer groups and payment terms aligned in both directions (Acumatica, no date shown). Amazon pricing is often set by a repricing tool rather than the ERP, so decide whether the ERP pushes a floor price or stays out of Amazon pricing entirely.

The control is an approval step before a price list change publishes to every channel at once.

Stage 5: Import orders and match customers

Order management owns this stage, and most daily exceptions appear here. Each channel order must become an ERP sales order with the right customer, items, location, tax and shipping charge.

Business Central’s documentation shows the decisions every connector forces. Customers match by email and phone or by bill-to address, or all orders go to one default customer, and if no customer matches and automatic creation is off, you must assign one manually. Shopify tax amounts are imported for reference and then recalculated in Business Central, and for US and Canadian localizations, if Shopify’s “include sales tax in product price and shipping rate” setting is on, imported orders cannot become sales documents (Microsoft Learn, September 30, 2026). The same page notes the connector tracks channel-liable (marketplace-collected) taxes separately, which matters for marketplace orders where the marketplace, not you, collects the sales tax.

Amazon orders carry an extra privacy step. Buyer names and shipping addresses are personally identifiable information, and an integration must request a Restricted Data Token through the Tokens API to retrieve them (Amazon SP-API, September 9, 2026).

What goes wrong: missed events. Shopify states that webhook delivery is not guaranteed, that ordering is not guaranteed, and that apps should run reconciliation jobs that fetch records changed since the last run (Shopify, no date shown). Ask any connector vendor how it catches an order that never triggered a webhook.

Stage 6: Send fulfillment and tracking back

The warehouse or 3PL manager owns this stage. When the ERP or WMS ships, the connector posts fulfillment and tracking back to the channel. Microsoft’s Shopify app and the BigSynapps and Folio3 BigCommerce-NetSuite connectors all list syncing fulfillment or shipment data back to the channel (Shopify App Store, no date shown; BigCommerce App Marketplace, March 2, 2023; BigCommerce App Marketplace, November 13, 2024).

Split shipments are the usual failure point, so test one before go-live. The control is an aging report of orders shipped in the ERP but not yet confirmed on the channel. If you also sell to retailers, the same shipment data feeds EDI documents such as the EDI 850 and its follow-on transactions.

Stage 7: Process returns and refunds

Customer service and accounting share this stage. Every channel refund should create an ERP credit memo tied to the original sale, and units return to stock only after inspection. Business Central imports return, refund and cancellation information with Shopify orders when configured (Microsoft Learn, October 20, 2025), and Celigo’s Shopify-NetSuite listing includes cancellations, refunds and returns (Shopify App Store, no date shown).

Stage 8: Reconcile payouts and settlements

The controller owns this stage. A Shopify Payments payout or Amazon settlement is a net deposit, and the ERP needs its gross components (sales, fees, refunds, reserves) to state revenue correctly. Business Central can import Shopify Payments transactions and payouts (Microsoft Learn, October 20, 2025).

Amazon settlement reports cannot be requested on demand. Amazon schedules them automatically, and integrations retrieve the current flat file V2 report through the Reports API (Amazon SP-API, September 9, 2026). Our guide to Amazon seller accounting shows the journal entries a settlement produces. The control is that every deposit in the bank matches a reconciled payout record to the cent.

Choosing the integration pattern and what it costs

Four patterns cover almost every project. The choice depends on how many channels you run and whether you have staff to maintain integrations.

Sources for the table: Shopify App Store Business Central listing, Microsoft pricing, BigSynapps listing, Celigo listing, Boomi pricing and Pipe17 pricing. Celigo’s own pricing page says its pricing is determined by endpoints and flows rather than data volume (Celigo, no date shown).

Native connectors are the cheapest start when your ERP vendor supports all your channels. Oracle lists Amazon Seller Central, Amazon Vendor Central, BigCommerce, Shopify, Walmart and others as NetSuite Connector storefronts (Oracle, no date shown). iPaaS tends to win when you run several channels plus a 3PL, a tax engine and a returns app, because one platform handles monitoring and retries for all of them.

One cost risk has eased. Amazon announced in November 2025 a $1,400 annual SP-API subscription and usage fees on GET calls, then said it “will not move forward with the SP-API usage and annual fees at this time” (Amazon, no date shown; PPC Land, May 14, 2026). Ask any Amazon connector vendor whether its contract lets it pass through future Amazon API charges.

Metrics to track

• Order exception rate: orders that failed to post on the first attempt, by channel and reason (unmapped SKU, missing customer, tax mismatch).
• Order sync latency: minutes from channel order to ERP sales order, with an alert tied to your shipping cutoff.
• Inventory sync lag: minutes from an ERP stock change to the channel update.
• Oversell count: orders cancelled because published stock did not exist.
• Unconfirmed shipments: orders shipped in the ERP but not marked fulfilled on the channel after a set number of hours.
• Payout reconciliation variance: bank deposits minus reconciled payouts and settlements, which should be zero at month end.

How software supports each stage

Native ERP connectors (Business Central, Acumatica, NetSuite) cover stages 2 through 6, with returns and payouts varying by connector. iPaaS tools such as Celigo and Boomi add error dashboards and retries across stages 5 through 8. Order hubs such as Pipe17 help when you route orders to several warehouses or 3PLs. For the wider stack around these tools, see our guide to the software needed to run an ecommerce business.

How we researched this

We reviewed the top-ranking pages for “ecommerce ERP integration” from NetSuite, Shopify and MConnect Media; none covered Amazon order and settlement mechanics, API limits or published connector prices. We then read vendor documentation from Microsoft, Shopify, BigCommerce, Amazon, Oracle and Acumatica, plus each named connector’s pricing page or app listing, on October 9, 2026. No vendor paid for inclusion.

Related guides

• NetSuite Amazon Connector: Seller and Vendor Central Options
• NetSuite Integration Options: SuiteTalk, RESTlets and iPaaS
• NetSuite for Retail: POS, Ecommerce and Inventory Guide

Frequently asked questions

Should the ERP or Shopify be the source of truth for inventory?

For most brands and distributors, the ERP should own available inventory because it sees warehouse stock, open B2B orders and receipts. Shopify then displays the quantity the ERP publishes.

Is iPaaS better than a native ERP connector?

A native connector is usually cheaper and faster to start if it supports all your channels. iPaaS costs more but monitors many systems in one place and lets you change mappings without waiting for the ERP vendor.

How do I bring Amazon orders into my ERP?

Use a connector that reads orders through Amazon’s Selling Partner API, maps seller SKUs to ERP items, and treats FBA stock as its own ERP location. Buyer address data requires a Restricted Data Token, so confirm the connector holds the right Amazon roles.

How much does ecommerce ERP integration cost?

Published prices run from a free app (Business Central’s Shopify connector) to $3,500 setup plus $2,880 per year for a BigCommerce-NetSuite connector, and $7,800 to $18,900 per year for Celigo’s Shopify-NetSuite editions. NetSuite Connector, Acumatica and Pipe17 do not publish prices. Add partner configuration and testing time to any license figure.

What breaks most often after go-live?

Unmapped SKUs, unmatched customers and tax differences are the most common order exceptions. Missed webhooks cause silent gaps, which is why Shopify recommends periodic reconciliation jobs.

Sources

• Microsoft Learn, Synchronize and fulfill sales orders (Business Central Shopify connector), September 30, 2026. learn.microsoft.com
• Microsoft Learn, Shopify connector overview, October 20, 2025. learn.microsoft.com
• Microsoft, Dynamics 365 Business Central pricing, no date shown, checked October 9, 2026. microsoft.com
• Shopify App Store, Dynamics 365 Business Central listing (Microsoft), no date shown, checked October 9, 2026. apps.shopify.com
• Shopify App Store, NetSuite Integration by Celigo listing, no date shown, checked October 9, 2026 (Celigo sells this product). apps.shopify.com
• Celigo, Pricing, no date shown, checked October 9, 2026. celigo.com
• Boomi, Pricing, no date shown, checked October 9, 2026. boomi.com
• Pipe17, Pricing, no date shown, checked October 9, 2026. pipe17.com
• Shopify, GraphQL Admin API rate limits, no date shown. shopify.dev
• Shopify, Webhook best practices, no date shown. shopify.dev
• Shopify, Ecommerce ERP integration, July 18, 2026 (Shopify sells the platform). shopify.com
• BigCommerce, API rate limits, no date shown. docs.bigcommerce.com
• BigCommerce App Marketplace, NetSuite ERP Connector by BigSynapps, March 2, 2023 (BigSynapps sells this product). bigcommerce.com
• BigCommerce App Marketplace, NetSuite ERP Connector by Folio3, November 13, 2024 (Folio3 sells this product). bigcommerce.com
• Amazon Selling Partner API, Settlement report type values, September 9, 2026. developer-docs.amazon
• Amazon Selling Partner API, Tokens API use case guide, September 9, 2026. developer-docs.amazon
• Amazon Selling Partner API, getInventorySummaries reference, September 9, 2026. developer-docs.amazon
• Amazon, Cancellation of SP-API fees, no date shown. developer.amazonservices.com
• PPC Land, Amazon drops SP-API fees after developer pushback, May 14, 2026. ppc.land
• Oracle, NetSuite Connector supported storefronts and 3PLs, no date shown. docs.oracle.com
• Acumatica, Commerce connectors, no date shown (Acumatica sells ERP software). acumatica.com
• NetSuite, ERP and ecommerce integration, March 10, 2026 (NetSuite sells ERP software). netsuite.com
• MConnect Media, ERP integration for ecommerce, April 7, 2023 (MConnect sells integration services). mconnectmedia.com

10578 Overall Score

Sherman Hsieh

CEO & Editor-in-Chief, Business-Software.com
Independent analysis of enterprise software — ERP, CRM and more

Sherman Hsieh is the founder, CEO, and editor-in-chief of Business-Software.com. He leads the site's independent, buyer-focused coverage of ERP, CRM, and other business systems, including vendor-neutral comparisons, pricing analysis, and implementation guidance. Before founding Business-Software.com, Sherman was an executive at Siebel ...