Integration combo
Shopify to FreeAgent integration
FreeAgent is the accounting platform a lot of UK Shopify merchants use to keep on top of VAT, MTD submissions and the year-end. The integration moves orders, customers and refunds out of Shopify and into FreeAgent as proper sales invoices and credit notes, with VAT treatment, tender and currency correct from the first run. We design, build and support Shopify-to-FreeAgent integrations as a certified Patchworks Partner Agency, so the accounting side stays in step with the storefront without manual reconciliation.
Flow shape
Sales posting: Shopify to FreeAgent
How a Shopify order lands in FreeAgent as a sales invoice with VAT, customer, and tender treatment in place from the first run.
- Trigger Shopify Order paid order/paid webhook
- Extract Patchworks Ingest payload queue, dedupe, normalise
- Transform Patchworks Resolve VAT rate standard, reduced, zero, exempt
- Decision Patchworks Customer exists? FreeAgent contact lookup
- Transform Patchworks Map to invoice line items, discounts, currency
- Action FreeAgent Create invoice marked paid against tender
- Writeback Shopify Tag order store FreeAgent invoice reference
Illustrative only. The diagram above shows how an integration of this shape works in concept. It is not a screenshot or export of the actual Patchworks process flow; the production flow has more nodes, more branches and more error handling than a marketing page can usefully render.
What we sync
3 synchronisations between Shopify and FreeAgent.
Only the data flows that both platforms actually support. Each section below describes what’s in scope, the gotchas we watch for, and how the flow is shaped inside Patchworks.
- 01
Order sync
Shopify FreeAgent
Orders raised in Shopify flow into FreeAgent on creation, status change and edit. The flow normalises Shopify's order schema into the record shape FreeAgent expects, including line-level discounts, taxes, gift cards, shipping methods and multi-currency. Partial cancellations and post-capture edits are handled with idempotent updates so FreeAgent stays the system of record without double-counting. Edge cases that come up most often on this pair: backorders, pre-orders, subscription rebills and orders placed through guest checkout with no matching customer record on the destination side.
- 02
Customer sync
Shopify FreeAgent
Customers created or updated in Shopify flow into FreeAgent with a stable cross-system identifier so the same shopper isn't fragmented into duplicates across the estate. Addresses, marketing preferences, B2B account hierarchies, tax exemption flags and channel attribution are mapped explicitly rather than left to FreeAgent's defaults. Where FreeAgent is the customer system of record (CRM or ERP) we publish back into Shopify so storefront personalisation and segmentation reflect the canonical state. GDPR deletion and rectification are propagated across the integration in both directions.
- 03
Refund sync
Shopify FreeAgent
Refund decisions raised in Shopify push into FreeAgent as the financial event they are, with original payment method, partial-versus-full handling, tax recalculation and currency intact. The flow waits on inspection outcome where the merchant policy requires it rather than firing on RMA creation. Refunds against gift cards, multi-tender orders and marketplace orders (where the marketplace owns the refund execution) each take a different path; the integration picks the right one based on the original order's tender mix rather than a single default rule.
Typical delivery
3 to 5 weeks for a standard delivery.
Up to 5× faster using PatchBuddy- Week 1 Discovery: VAT scheme, MTD requirements, tender mapping, customer-resolution policy.
- Weeks 2 to 3 Build: order, customer and refund flows in Patchworks.
- Week 4 Integration testing using staged Shopify orders against a FreeAgent sandbox; UAT with finance.
- Week 5 Cutover and hyper-care; transition into support retainer with monitoring and SLA.
Patchworks delivery
How Patchworks shapes Shopify to FreeAgent.
FreeAgent's API is clean but opinionated about how invoices, customers and tax rates should look. The work is in shaping Shopify order events into the right FreeAgent constructs while respecting the MTD reporting rules HMRC enforces. We build the Shopify-to-FreeAgent flows in Patchworks with explicit VAT rate mapping, tender-aware refund handling and a customer-resolution step so the FreeAgent ledger doesn't fragment into duplicates over time.
Got more connectors that need to live in this flow? A 3PL, a marketplace, returns, a PIM, anything. We can do it. Most live integrations end up larger than a pair, all built and supported as one estate. More on multi-platform estates →
Our Patchworks practiceQuestions
Common questions.
-
01 How is VAT handled across rates?
Each Shopify tax line maps to a FreeAgent VAT rate explicitly: standard, reduced, zero-rated, exempt, outside the scope. We agree the mapping during scoping, so MTD submissions reflect the same VAT treatment finance expects to see on the FreeAgent VAT return. -
02 What about refunds and partial refunds?
Refunds post as credit notes in FreeAgent against the original invoice. Partial refunds map to line-level credit notes; restocking fees and gift-card refunds get the right tax treatment rather than collapsing into a single adjustment. -
03 Does the integration support Shopify Markets and multi-currency?
Yes. Orders post to FreeAgent in the order currency with FX policy applied at the configured rate. We agree the rate source during scoping so finance isn't reconciling two interpretations of exchange rates. -
04 How are Shopify customers reconciled to FreeAgent contacts?
Email plus an external identifier is the typical merge key. New customers create FreeAgent contacts on first order; existing customers reuse the same contact across all subsequent orders so the ledger stays clean. -
05 Do you support Shopify-to-FreeAgent under SLA after go-live?
Yes. The same team that builds the integration runs it under retainer. Monitoring on every shipped flow, on-call cover, monthly health checks and tiered response SLAs from £750/month.
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