Stripe + e-conomic integration: the complete guide

If you take payments with Stripe and keep your books in e-conomic, you already know the monthly ritual: export a report, squint at the payouts, work out which fees belong where, and hand-key vouchers until the Stripe balance finally ties out. This guide explains what a proper Stripe → e-conomic integration actually books for you, and what to configure so every entry is correct from day one.

Why manual Stripe bookkeeping is so painful

Stripe is a payment processor, not a ledger. A single paid invoice in Stripe touches several accounts in your bookkeeping: the revenue, the VAT, the processing fee Stripe kept, and — days later — the payout that lands in your bank. Do this by hand and a few things always go wrong:

• Fees get lumped into one number instead of booked against a fee account, so your Stripe balance never quite reconciles.
• Invoices in foreign currency settle at a different rate than they were issued, and the exchange difference goes unrecorded.
• Payouts are booked as a lump sum with no link back to the invoices they paid.
• Refunds are forgotten, or booked as negative revenue instead of a proper credit note.
• VAT on cross-border sales is guessed at rather than resolved from the customer's country and VAT number.

None of this is hard, exactly — it's just repetitive, easy to get slightly wrong, and it scales linearly with your transaction count. Automation removes the ritual entirely.

What an automated sync books for you

A good integration doesn't dump a monthly summary into e-conomic — it posts real, reconcilable entries for each event, exactly as a careful bookkeeper would. Here is what BookSyncer books:

Invoices

When a Stripe invoice is finalized, the matching customer is created in e-conomic (if it doesn't exist yet) and an invoice is raised. You decide whether it lands as a draft for review or is booked automatically — a single toggle per pipeline.

Payments — with the correct exchange rate

When the invoice is paid, a customer payment voucher is booked against your debtor (accounts receivable) account. If the invoice was issued in one currency and paid in another, the payment is recorded at the rate that actually applied at settlement — not the invoice-date rate — so the amounts match reality.

Stripe fees

The processing fee Stripe deducts is booked to your fee account as a finance voucher. This is the step most manual workflows skip, and it's the reason the Stripe clearing account never reconciles: the gross invoice, the fee, and the net settlement have to be booked separately for the numbers to tie out.

FX differences

Any currency gain or loss between the invoice and the settlement is posted to your FX gain/loss accounts automatically. No month-end currency adjustment, no manual journal.

Payouts to your bank

When Stripe pays your balance out to your bank, a journal entry moves the amount from your Stripe clearing account to your bank account. Your Stripe clearing account trends back toward zero, exactly as it should, and the payout is traceable to the activity behind it.

Credit notes on refunds

A refund creates and books a credit note against the original invoice — the correct treatment, rather than a negative sales line. (Full refunds are handled end to end; partial refunds are flagged for manual review rather than booked incorrectly.)

Getting VAT right: zones and reverse charge

For a Danish SaaS or e-commerce business selling across borders, VAT is where automation earns its keep. The right treatment depends on where the customer is and whether they have a valid VAT number:

• Zone 1 — domestic (Denmark): standard 25% Danish VAT (moms).
• Zone 2 — EU with a valid VAT number: reverse charge (omvendt betalingspligt), VAT 0%, and the customer accounts for it in their own country.
• Zone 3 — outside the EU: no EU VAT.

A proper integration resolves the zone from the customer's country and VAT number, validates EU VAT numbers so reverse charge is only applied when it's genuinely valid, and sets the matching e-conomic VAT code on the invoice. Our VAT reference goes into the detail, and the reverse-charge guide covers the rules from a founder's point of view.

A configuration checklist

Before you switch a sync on, you'll want these in place in e-conomic — most of them are a one-time pick from a dropdown during setup:

• A journal for your Stripe entries.
• Your debtor (accounts receivable) account.
• A Stripe clearing/balance account to hold funds between payment and payout.
• A fee account for Stripe's processing fees.
• FX gain/loss accounts for currency differences.
• The bank account your payouts land in.
• Your VAT zones and codes, plus any overrides for edge-case customers.
• Optional: customer group, payment terms, invoice layout(s), and product mappings from Stripe products to e-conomic product numbers.
• Your draft vs. auto-book preference, and a historical start date if you want to catch up past invoices.

The five-minute version

You don't have to build any of this yourself. BookSyncer connects to Stripe (read-only, through Stripe Connect) and to your e-conomic agreement, and books everything above automatically — with a full audit trail for every event. If you'd rather see it than read about it, the setup guide walks through connecting both ends in about five minutes, and pricing starts free.