FreshBooks' app store covers the common integrations well enough for most freelancers and small service businesses: Gusto for payroll, a short list of CRMs, Shopify for e-commerce invoicing, and Zapier for lighter no-code automation between FreshBooks and a few thousand other apps.
Once a business needs something the app store doesn't cover, a specific CRM Zapier only partially supports, a bank feed with mapping logic that's specific to how the business categorizes expenses, a project tool that needs two-way sync rather than one-off triggers, the work moves to FreshBooks' own REST API.
The API covers the core objects a business actually needs to automate around: clients, invoices, expenses, time entries, and payments, authenticated through OAuth. It's a real, documented API, not a workaround, which makes most of what we build here straightforward custom development rather than anything fragile.