What happens when a client pays a FreshBooks invoice through Stripe?

ml-connector receives the payment event from Stripe, correlates it to the matching FreshBooks invoice by customer and amount, and records the payment in your FreshBooks accounting. The invoice remains in FreshBooks for your records, but the payment is now visible in both systems.

Does ml-connector write invoice status or payment details back to FreshBooks?

No. FreshBooks computes invoice status based on payments, so ml-connector does not write status updates back. Instead, it tracks what Stripe collected and reconciles it against FreshBooks during each sync cycle so the two stay in agreement. This prevents duplicate-entry issues and respects FreshBooks' read-only status logic.

How does the integration handle FreshBooks OAuth2 and Stripe API Key authentication?

During setup, ml-connector requests OAuth2 authorization from a FreshBooks user account (Authorization Code grant with specific scopes), stores the token encrypted, and refreshes it when the API returns an auth error. The Stripe API Key is also encrypted at rest. Both credentials are kept separate and used only for their respective API calls.

FreshBooksStripe

FreshBooks and Stripe integration

FreshBooks records your invoices, expenses, and clients. Stripe collects payments online. Connecting them means a customer paying an invoice in Stripe automatically updates that invoice status in FreshBooks, and new invoices you create in FreshBooks appear in Stripe ready to collect payment. Your accounting and payments stay aligned with no manual entry, and you get a complete audit trail of every sync.

How FreshBooks works

FreshBooks exposes invoices, payments, clients, expenses, bills, and chart of accounts through a REST API at https://api.freshbooks.com. It uses OAuth2 Authorization Code grant with user-delegated credentials (not Client Credentials) and requires specific scopes per resource. Webhooks notify on invoice, payment, client, and expense events via POST to your endpoint with HMAC-SHA256 signature. FreshBooks does not support Purchase Orders as a resource, and invoice status is read-only (computed by the system). Webhook delivery ranges from seconds to several minutes and times out after 10 seconds per attempt.

How Stripe works

Stripe exposes customers, invoices, charges, payment intents, subscriptions, and payouts through REST endpoints at https://api.stripe.com/v1. Authentication uses API Key (secret key) sent via HTTP Basic Auth or Bearer token; there is no OAuth2 for server-to-server integration. Stripe delivers webhook events with at-least-once semantics and a v1 HMAC-SHA256 signature, with a 5-minute replay window and retries for up to 3 days. Stripe has no vendors, suppliers, GL accounts, or employee records. Payment updates use POST not PUT, and prices are immutable after creation.

What moves between them

The main flow moves FreshBooks invoices and clients to Stripe. When a client is created or updated in FreshBooks, ml-connector upserts a matching Stripe customer with the same billing details. When an invoice is created in FreshBooks, ml-connector creates a Stripe invoice and links it to the customer. Payments received in Stripe update the invoice status in FreshBooks so your accounting records reflect what was actually collected. The sync runs on a configurable schedule and also captures FreshBooks webhook events in real time.

How ml-connector handles it

ml-connector stores the FreshBooks OAuth2 token (obtained during setup with user authorization) encrypted, and refreshes it when the API returns an authorization error. The Stripe API Key is also encrypted at rest. Because FreshBooks webhooks are user-delegated and require a pre-authorized account, ml-connector uses that delegated session to read FreshBooks data and polls for incremental changes on a schedule. Stripe webhook events are received and correlated to FreshBooks invoices to track payments. Since FreshBooks invoice status is read-only (computed by the system), ml-connector does not write status updates back to FreshBooks; instead, it tracks payment state in Stripe and reconciles it against FreshBooks records during each sync cycle. Rate limits on both sides are respected with backoff and retry. Every invoice and payment carries a full audit trail for troubleshooting and replay.

A real-world example

A small-to-mid-size consulting firm uses FreshBooks to manage client invoicing and track time, and Stripe to accept online payments from clients worldwide. Before the integration, the finance team reviewed Stripe payments daily, then logged into FreshBooks to mark invoices as paid by hand. Reconciliation was manual and error-prone, especially when a partial payment arrived or a customer paid in a different currency. With FreshBooks and Stripe connected, every payment in Stripe immediately reflects in FreshBooks, invoices appear in Stripe ready to collect, and the firm's accounting is reconciled in real time. Month-end close is faster because there is no payment-matching backlog.

What you can do

Sync FreshBooks clients to Stripe customers with matching billing details so payment collections are attributed to the right account.
Create Stripe invoices from FreshBooks invoices automatically, with line items and amounts ready for payment collection.
Track payments received in Stripe and reconcile them against FreshBooks invoice records so your accounting shows the true collection status.
Authenticate FreshBooks with OAuth2 user-delegated credentials and Stripe with API Key, bridging two different auth systems.
Poll FreshBooks on a configurable schedule and capture real-time webhook events from both systems, with full audit trail and error replay.

Questions

What happens when a client pays a FreshBooks invoice through Stripe?: ml-connector receives the payment event from Stripe, correlates it to the matching FreshBooks invoice by customer and amount, and records the payment in your FreshBooks accounting. The invoice remains in FreshBooks for your records, but the payment is now visible in both systems.
Does ml-connector write invoice status or payment details back to FreshBooks?: No. FreshBooks computes invoice status based on payments, so ml-connector does not write status updates back. Instead, it tracks what Stripe collected and reconciles it against FreshBooks during each sync cycle so the two stay in agreement. This prevents duplicate-entry issues and respects FreshBooks' read-only status logic.
How does the integration handle FreshBooks OAuth2 and Stripe API Key authentication?: During setup, ml-connector requests OAuth2 authorization from a FreshBooks user account (Authorization Code grant with specific scopes), stores the token encrypted, and refreshes it when the API returns an auth error. The Stripe API Key is also encrypted at rest. Both credentials are kept separate and used only for their respective API calls.

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