Connecting your system to accounting: invoices and payments in one flow

Where an invoice gets stuck

The order is in the system or in a spreadsheet. The invoice is created in the accounting package. Between them sits a person typing the name, the tax number, the address, the line items and the amounts a second time. The more invoices a month, the longer the customer waits for the document and the more typos land in tax numbers.

Then the bank transfers arrive. Someone opens the bank, reads the payment references and works out which invoice each one belongs to. Customers put the order number in the reference, or the invoice number, or their own company name, or nothing. At month end the list of unpaid invoices does not match what came in, and the phone calls start.

Add an external bookkeeper, if you have one. Sales invoices are collected from the package, purchase invoices from emails and a drawer, and the bundle goes out once a month. Closing the month waits until the bookkeeper has the last invoice from the drawer and has asked about the missing ones.

What an accounting connection looks like

The connection I build is made of a few flows. Each can go live on its own.

An invoice from the order data

The invoice is created in the system from data that is already there: customer, items, prices, payment method. It reaches the accounting package as a finished document. Numbering stays in one place so there are never two invoices with the same number. Credit notes follow the same route.

E-invoicing where the law requires it

If you have a Polish company, invoices between businesses pass through KSeF, the national e-invoicing system; confirm the deadlines and the exceptions, which depend on company size, with your accountant. Your own system can send invoices to KSeF directly and receive the number it assigns, or hand that over to an accounting package that already does it. Purchase invoices come back from KSeF the same way, so nobody collects them from emails. Other countries have their own schemes, and the same connection pattern applies.

Payments matched on their own

The system pulls the list of transfers from the bank or the payment provider and matches them to invoices by number, amount and payer name. Whatever matches closes on its own. Whatever does not lands on a short list for a manual check. A salesperson sees in the system that the customer has paid, without asking the bookkeeper. Reminders for overdue payments go out on their own, on agreed days.

A bundle for the bookkeeper

When an external bookkeeper keeps the books, the system prepares on an agreed day a complete set of documents in a format they load in one go: sales invoices, purchase invoices, a bank statement with payments already matched. The bookkeeper gets a complete set, and you collect nothing.

Which packages can be connected

Every accounting package I have worked with allowed some form of connection, but not the same one. Some offer a direct connection. Others only load and export files in their own format. Before quoting I check exactly what your version can do, because differences between versions of the same package can be large.

Before we start I also check the accounting vendor’s terms: some charge separately for the ability to connect to other programs, or per document loaded from outside. Better to know before building than after.

What can go wrong

Two sources of numbering. Invoices issued both in the system and in the accounting package will sooner or later get the same number. We agree one place that numbers, and the other only receives.

An invoice sent twice. The accounting package did not respond, the system retried, the invoice went in twice. The connection remembers what it has already sent and checks before every attempt.

A payment matched to the wrong invoice. Two invoices for the same amount to the same customer. The system does not guess; it shows both for a manual choice. Five minutes of checking beats a wrong balance.

Changes in the rules. E-invoicing schemes and document formats change. I leave the connection with documentation, and under ongoing care I check it after every major change.

Where to start

The biggest gain comes from invoices built from order data, because that flow carries the most documents. Payment matching is the second stage; it cuts the list of unpaid invoices down to the ones you need to chase. The bookkeeper’s bundle comes last.

How the accounting connection fits with the other flows in the company is on the main page of the guide and on the page about connecting a shop to the warehouse and couriers. If your accounting package cannot connect other than by clicking, see the page about programs without a connection.

Tell me in the form below which accounting package you use, how many invoices a month you issue and whether the books are kept in-house or by a bookkeeper. I will get back to you.