Switching accounting software mid-year: what to keep for the ATO, your payroll and your next loan

A lot of Australian businesses are changing accounting software this year. Some are moving because an old desktop file stopped working. Some are moving because payroll got harder after 1 July. Others just want bank feeds, invoicing and payroll in one place. Very few stop to think about what the move does to their BAS, their STP reporting, or the next time a lender asks to see their numbers.

This guide is the plan we’d want a client to follow. It covers when to cut over, what to finish in the old system first, how to keep payroll clean, and which reports to save before you cancel anything.

Why are so many businesses switching software in 2026?

Three changes have pushed a lot of owners to move mid-year rather than wait for next July:

• MYOB’s offline files. MYOB’s help centre says AccountRight PC Edition stopped supporting offline company files from 17 June 2026. To open an old offline backup you need AccountRight v2026.4, the last version that works with them. If your books lived in a desktop file, you now need either the cloud version or something else.
• The Small Business Superannuation Clearing House closed. The ATO confirms the SBSCH closed permanently on 1 July 2026 as part of the Payday Super reform, and it can no longer be used to make payments or download records. Many small employers who paid super that way have since moved to payroll software with super payments built in.
• Payday Super itself. Super now has to be paid with each pay run, not quarterly, and reported through Single Touch Payroll every payday. Spreadsheets and older payroll setups struggle with that rhythm.

None of these force a bad switch. But a rushed switch is where things go wrong.

When is the best date to cut over?

Pick a date that lines up with your BAS. Each quarter’s GST should come from one system, not be stitched together from two.

Cut-over date	How it works	Watch out for
1 July	Cleanest. New financial year, new STP year, nothing to split.	Waiting may not be an option if your old software has stopped working.
1 January	The usual mid-year choice. October to December closes in the old system, and the new one starts with a full quarter.	Payroll year-to-date figures must move across (see below). Christmas leave and holiday pay runs make December a bad month to test anything new.
1 April or 1 October	Also fine, because both start a BAS quarter.	Same payroll issue as 1 January.
Mid-quarter	Avoid.	One BAS built from two ledgers, plus a higher chance of missing or double-counting GST.

If you’re reading this in late October, 1 January gives you about ten weeks to set up the new file, run it alongside the old one for a month, and lodge the December quarter BAS from the old system.

What should you finish in the old system before you switch?

Close the old file properly. Loose ends at cut-over turn into reconciling problems for months.

1. Reconcile every bank account to the cut-over date. Bank, cards, loan accounts and clearing accounts for Stripe, Square or PayPal.
2. Lodge, or at least prepare, the last BAS from the old system. Keep the GST reports and workpapers with it.
3. List every open invoice and bill. These become your opening receivables and payables. If you report GST on a cash basis, take extra care: an invoice raised in the old system but paid after the cut-over must be counted in the new system’s BAS. Missing it underpays GST. Counting it twice overpays.
4. Run the final pay run of the period in the old system, including super, before payroll moves.
5. Note the GST settings and tax codes. Accounts basis (cash or accrual) and GST reporting frequency must match in the new software.

How do you move payroll without upsetting STP and Payday Super?

Payroll is where mid-year switches most often go wrong. That’s because the ATO and your employees both see the result.

The ATO identifies each STP report by your ABN, branch number and the software’s business management software ID (the BMS ID). It shows employees one income statement for each combination. Its guidance on changing your payroll solution gives you two clean paths:

• Carry year-to-date amounts across. If the new software uses a different BMS ID, you need to give the ATO the previous BMS ID (where the software lets you), or zero out the year-to-date amounts in the old software. The ATO lists forgetting this as a common mistake. The result is duplicate amounts on employees’ income statements.
• Don’t carry year-to-date amounts across. The new software starts at zero and the ATO shows a separate income statement for each system. That’s acceptable, but both must be finalised at year end.

Ask your new software provider which approach it supports before the first pay run. Then add the Payday Super check. The first pay run in the new system must also send super correctly. Fund details, member numbers and SuperStream settings need to be right, or contributions can bounce back after payday. Run a small test pay run, or run payroll in both systems for one cycle, before you rely on it. Our page on payroll and Payday Super covers the cash flow side of paying super every payday.

What does a lender see after you switch?

This is the part most migration checklists skip, and it matters to a business that may borrow in the next year or two.

When you connect accounting software to a loan application, the lender’s system pulls reports such as profit and loss, balance sheet and aged receivables. A freshly converted file often holds:

• only a few months of transaction detail (conversions often bring across limited history, with older periods as summary balances);
• opening balances posted as journals, which can look odd to someone who doesn’t know a switch happened;
• a renamed or simplified chart of accounts, so income lines don’t match last year’s reports;
• the same customers, but with old invoices missing.

None of that is a problem if you explain it and can show the history. It becomes a problem when the old subscription has lapsed and the history is gone. Lenders still read your bank statements for trading history, but larger facilities, lines of credit and invoice finance often need the accounting reports too.

If you think you’ll need finance in the next year, check where you stand now, before the cut-over. It’s a short enquiry, and it’s easier to talk through your numbers while everything still sits in one system.

Which reports should you export before cancelling the old software?

Export these as PDF and spreadsheet files and store them with your tax records:

• Monthly profit and loss for the last 24 months, plus full-year reports for the last two financial years.
• Balance sheet at the cut-over date and at each of the last two 30 June dates.
• Aged receivables and aged payables at the cut-over date, with invoice-level detail.
• GST reports and BAS workpapers for every quarter in the old system.
• Payroll summaries: year-to-date by employee, super paid, leave balances and STP lodgement history.
• General ledger detail for the current and previous financial year.
• A full backup of the company file, plus a note of the software version needed to open it.

Then decide how you’ll keep access. Business.gov.au says you “need to keep most business records for 5 years”, and some company and employee records for 7. A backup file you can’t open doesn’t meet that need. Many providers offer a cheap read-only plan. If you’re coming from AccountRight desktop, keep a copy of the version that can still open your backups.

Illustrative example: a clinic moving at the half-year

This is a made-up scenario to show the sequence, not a client story.

A physiotherapy clinic with nine staff has run on AccountRight desktop for years and paid super through the SBSCH. In July it scrambles to set up a commercial clearing house, then decides to move bookkeeping and payroll to cloud software on 1 January.

In November and December it builds the new file, maps its practice software’s daily takings to the new chart of accounts, and runs December’s payroll in both systems to compare. It lodges the October to December BAS from AccountRight and exports 24 months of monthly profit and loss, the 31 December balance sheet and aged receivables from health funds and NDIS plan managers. It keeps a read-only copy of the old file.

In March the clinic wants a line of credit to buy a second treatment room’s equipment. The lender connects to the new file and sees ten weeks of data. The owner uploads the exported reports with a two-line note: “Converted from AccountRight on 1 January 2027; history attached.” The lender reads the full picture straight away, and the application keeps moving.

What mistakes cost the most?

• Cutting over mid-quarter. You end up building one BAS by hand from two ledgers.
• Double-counting cash-basis GST on invoices raised before the switch and paid after it.
• Duplicate STP year-to-date figures, which leave staff confused at tax time and create correction work for you.
• A missed super payment in the first new pay run. Under Payday Super, late contributions can mean a super guarantee charge, which costs more than the super itself.
• Cancelling the old subscription too early and losing access to records you must keep for years.
• Switching during a loan application. The accounting reports won’t match the bank statements while you’re half-converted.

If you want to see how a lender would read your numbers once the dust settles, our guide to reading your numbers like a lender walks through it. The online readiness check shows what you’d still need to gather.

New software, clean books. A good moment to line up funding.

A software switch is one of the rare times every number in the business gets checked, reconciled and exported. That makes it an ideal moment to find out what finance you could access, whether that’s a standby line of credit for the next busy season or a loan for the upgrade that prompted the move. We work with businesses on Xero, MYOB, QuickBooks and practice software every day, and a recent conversion doesn’t faze us when the history is there.

The online enquiry takes about 60 seconds. Asking doesn’t touch your credit file, because there’s no credit check when you first enquire. We don’t send your details to a pile of lenders either, so you won’t get a flood of calls. A real person reads your enquiry, looks at your situation, including where you are in the switch, and calls you back. Please fill the form in accurately, especially your monthly turnover and how long you’ve been trading, so we can match the right option first time.

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