How to switch accounting software with minimal disruption to invoicing and payroll

Switching accounting software can feel like moving house: awkward, time-consuming and a little terrifying when you think about what might get left behind. I’ve helped dozens of small businesses make the jump — from sole traders to micro-limited companies — and I’ve seen the same issues come up each time. In this post I’ll walk you through a practical, step-by-step approach to switch accounting software with minimal disruption to invoicing and payroll. I’ll include the checks and templates I use in practice, plus tips for common UK tools like Xero, QuickBooks, FreeAgent, Sage and payroll apps such as BrightPay or built-in Xero/QuickBooks payroll.

Decide why you’re switching and set realistic goals

Before you start exporting data or cancelling subscriptions, be clear about why you’re moving and what ‘success’ looks like. Common reasons include:

• Better automation for bank feeds and reconciliation (e.g. Xero or QuickBooks Online)
• Simpler invoicing workflows or client portals
• Integrated payroll or better compatibility with your payroll supplier (BrightPay, IRIS, etc.)
• Cost reduction or better reporting for management decisions

Set simple, measurable goals: for example, “All open sales invoices migrated and outstanding aged correctly,” or “Payroll continuity for the next RTI submission with no duplicate payments.”

Plan timing carefully — avoid month/quarter ends and payroll days

Pick a quiet period to switch. I recommend doing go-live mid-month after a clean reconciliation up to the last bank statement date, and not in the middle of a payrun week. For UK businesses, avoid switchovers that cross a scheduled RTI submission or a payroll date. Build two weeks of runway: one week to prepare and export, and one week to test and fix issues after go-live.

Pre-migration checklist

• Reconcile bank accounts to the last statement date and note the ledger balances.
• List outstanding sales and purchase invoices and their aged positions.
• Export payroll data for current tax year (employee records, year-to-date payments, tax codes).
• Backup the current accounting system and save export files securely.
• Confirm HMRC settings for PAYE and any payroll provider integrations.
• Gather lists of customers, suppliers, product/service codes and chart of accounts mapping.
• Agree a cut-off date and communicate it to staff and regular suppliers/customers.

Export what you need — and only what you need

Not everything needs to move. The aim is to retain continuity for invoices, receipts, VAT and payroll where necessary. At minimum export:

• Chart of accounts
• Customer and supplier lists (with contact, email and payment terms)
• Open sales and purchase invoices (with invoice numbers, dates, amounts, and outstanding balances)
• Bank statements, reconciled balances and unpresented cheques
• VAT returns history and any partial exemption calculations
• Payroll employee master data and year-to-date figures

Most modern packages let you export .CSV or .XLS files for customers, suppliers, and nominal ledgers. For payroll, export employee details, pay history and employer payment summaries. If you use BrightPay, you can export RTI submissions and employee P60/P45 information.

Map data fields — create a mapping table

Different systems use different field names and account codes. Create a simple mapping table to avoid surprises. Here’s an example I use with clients:

Decide how to handle historic data

I often advise clients to bring across open balances and the current year-to-date VAT/payslips. For closed historic transactions, you can either import everything (time-consuming and expensive) or keep a read-only archive of your old system as a reference. Most small businesses find it’s enough to:

• Import the opening balances for the current year
• Bring across all open invoices and credit notes
• Keep PDFs of past invoices and bank reconciliations stored in cloud storage and link them from the new system where possible

Test in a sandbox — then do a controlled go-live

Use a demo or trial account in your new software. Import a small sample (one customer, one supplier, a couple of invoices) and reconcile a bank payment to see how it behaves. Test these specifically:

• Invoice generation and client emails (including branding)
• Payment allocation and bank reconciliation
• Payroll run for one employee and RTI submission flow (test only — don’t submit live RTI until ready)

If your new provider offers migration services (many do: Xero, QuickBooks and FreeAgent partners offer onboarding), use them for the heavy lifting. For payroll, coordinate with your payroll software vendor (BrightPay or provider) to import employee records and ensure PAYE references match HMRC.

Communicate with your clients and staff

Simple communication prevents confusion. Send a short note to customers saying invoicing will continue as usual but with a new system (include the same invoice numbers and payment details). For staff, outline what changes they’ll see (e.g. timesheet links, payslip access via a portal) and provide a short runbook for how to submit expenses or request payroll changes.

First month checks — what to reconcile immediately

• Bank statement balances match the opening balance in the new system
• All open invoices show correct outstanding amounts and ageing
• Payroll year-to-date and tax payments align with HMRC records
• VAT settings and return periods are set correctly

Switching accounting software doesn’t have to be disruptive if you prepare, map your data, test carefully and communicate clearly. If you’d like, I can help you review your migration plan or check the export files before you import them — drop me a note and tell me which systems you’re moving from and to, and your preferred go-live date.