bexio and Shopify: Integration for Swiss Small Businesses

bexio runs the books for 100,000+ Swiss small businesses. How Shopify orders become bexio invoices at the right VAT rate, and how its API connection stays signed in.

bexio is cloud business software for Swiss small businesses. Accounting, quotes and invoices, banking, payroll, contacts, products, stock and project time tracking all sit in one place, across four plans from Basic to Ultimate.

It started in Rapperswil-Jona in 2013 as easySYS and took the name bexio in 2015. Die Mobiliar, the Swiss insurer, announced its purchase in 2018, and bexio is now wholly owned by Mobiliar. That same announcement puts its customers at more than 100,000, with more than 7,000 fiduciary and accounting firms working with it as partners.

Made for Swiss paperwork

The Swiss details are built in. Invoices go out as QR invoices, more than 65 Swiss banks connect directly, and VAT is posted at the right rate automatically. Payroll is Swissdec-certified, and data is kept in Swiss data centers.

bexio was certified to ISO/IEC 27001 for information security in September 2026. Its AI features are growing too: it announced the acquisition of Kontera, an AI bookkeeping tool, in October 2025, and added AI document extraction to its packages in 2026.

Apps and connectors

The bexio Marketplace, relaunched in November 2024, lists more than 100 apps. Shop connectors such as the Shopify Connector by Helvy sit alongside HubSpot and a Zapier connector for lighter jobs.

How Shopify orders become bexio invoices

A Shopify connector turns each order into a bexio document. The Helvy connector, for example, creates and sends a bexio invoice for every Shopify order, with rules for several VAT rates and customer currencies. It keeps customers and products in sync as well.

VAT is the part that has to line up. Every line on a bexio invoice points to one of the company’s active sales tax rates, so each tax rate in Shopify needs a match in bexio. A shop selling books or food alongside other goods charges both the normal rate of 8.1% and the reduced 2.6%, and each needs its own match.

Prices need the same care. A bexio invoice can treat its amounts as including VAT or add VAT on top. A shop that shows prices with VAT included needs its invoices set the same way, or the totals in bexio come out higher than what the customer paid.

bexio’s REST API, versions 2.0 to 4.0

bexio’s API is REST with JSON, documented in English, with endpoints across versions 2.0, 3.0 and 4.0. Invoices, accounting, contacts, payments and payroll are all covered, with a Payroll API added in December 2024 and newer payment endpoints in 2025.

Apps sign in with OAuth 2.0. For a business’s own scripts, personal access tokens replaced the old API tokens in October 2024. They last 60 days, and anything shared with another party uses the full OAuth sign-in instead.

bexio limits requests per company per minute and tells the integration how many it has left with every response. Integrations check for changes on a schedule, and developers test against a trial account, which is free for 30 days.

Keeping a bexio connection running

An app stays signed in to bexio with a refresh token, which it only receives if it asked for the offline_access permission when the business first approved it. The permissions are fixed at that point. Refreshing a token keeps the same scopes, and adding new ones means going through the approval again. That matters when bexio changes the scopes an endpoint needs, as it did for its purchase bill and expense endpoints, among others, in June 2026.

The sign-in itself has moved before. bexio’s old login server at idp.bexio.com was switched off on March 31, 2025, after a six-month migration window. In September 2025, it marked its 3.0 payment endpoints for deprecation in favor of new 4.0 ones.

Contacts changed shape too. Since December 2025, anything creating or editing a contact sends the street name and house number as separate fields, while the old single address field still comes back in responses.

Shop orders into the books

bexio sits at the end of most of a Swiss small business’s paperwork, so it has a lot to receive. Shopify orders can arrive as invoices at the right VAT rate, payouts can be matched to the orders inside them, and a won deal in the CRM can become a quote without retyping.

Each of those runs on the same API and the same signed-in connection, which makes the scopes chosen on day one worth getting right. If someone types shop orders into bexio today, here’s how to put a number on it.

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