BAS Checklist 2026: 10 Steps to Lodge an Accurate BAS or IAS in QuickBooks

Ready to lodge your BAS with the ATO? Before you do, it pays to make sure every sale and expense for the period is captured and coded correctly in QuickBooks Online. A few minutes of checking now saves hours of amendments - and ATO queries - later.

Getting it right matters more in 2026. The penalty unit rose to $364 on 1 July, so a late BAS can now cost a small business up to $1,820. ATO interest on late payments is no longer tax‑deductible. And the ATO is moving businesses with a poor compliance history from quarterly to monthly BAS - three times the admin. An accurate, on‑time BAS is the simplest way to stay off that list.

This checklist follows the new QuickBooks Online interface. Most tax tasks now live under All apps > GST, and each step links to the QuickBooks help article that’s kept up to date if a menu moves.

Before you start

Three settings to confirm before you run a single report:

1. All transactions for the period are in QuickBooks - via bank feeds, imported files or manual entry - and nothing is sitting unreviewed under Banking.
2. Every report you run uses the same date range as the statement period you’re reporting.
3. GST settings show the accounting method you’re registered for with the ATO - Cash or Accrual. QuickBooks reports default to Accrual unless your GST preference is set to Cash, and mixing the two is the most common reason a BAS doesn’t tie back to the balance sheet.

1. Reconcile every bank, loan and credit card account

Go to All apps > Accounting > Reconcile, pick each account from the dropdown and match transactions to the statement until the difference is $0.00. Do this for bank accounts, loan accounts and credit cards. If an account won’t reconcile, stop and investigate - an unreconciled account usually means missing, duplicated or mis‑dated transactions, and any of those can mean a BAS revision later.

• Difference is $0.00 for every account at the period end date
• No unreconciled items older than the current period
• Transfers between your own accounts recorded as transfers, not income or expenses

Help article: Reconcile an account in QuickBooks Online

2. Capture petty cash and cash expenses

Cash expenses don’t arrive through a bank feed, so they’re easy to miss. Post them through a Petty Cash (or similar) account with the correct GST code. The QuickBooks mobile app lets you snap the receipt on the spot, so the transaction and its evidence land in QuickBooks together.

• All cash receipts for the period entered and coded
• Petty cash balance in QuickBooks matches cash on hand

3. Separate personal expenses and private use

Anything personal paid from a business account must not be claimed as a business expense or GST credit. Post the personal portion to Drawings (sole traders and partnerships) or a Director’s/Beneficiary Loan account (companies and trusts), coded Out of Scope. Where an expense is partly business - a phone plan, a vehicle, home internet - claim only the business percentage and code the private share Out of Scope.

• Personal transactions moved to Drawings or the relevant Loan account
• Mixed‑use expenses split by business percentage
• Private portions coded Out of Scope (not GST‑free)

4. Review debtors and creditors

Go to Reports > Standard reports and run Accounts receivable ageing summary (under Who owes you) and Accounts payable ageing summary (under What you owe). Look for duplicate invoices or bills, payments applied to the wrong invoice, and old balances that were actually paid or written off. If you report on an Accrual basis these balances feed straight into your GST figures.

• No duplicate invoices or bills
• Payments allocated to the correct invoice/bill
• Stale balances investigated, corrected or written off

Help article: Run an accounts receivable ageing report

5. Check new asset and finance purchases

Bought a vehicle, equipment or other capital item this period? Check the invoice is coded GST on Capital (not Non‑Capital) so it lands at G10 rather than G11 on your BAS, and that the GST amount matches the tax invoice. If the purchase was financed, make sure the chattel mortgage, hire purchase or lease is posted correctly - GST is generally claimed up front on a chattel mortgage but treated differently on a lease. If you’re unsure, confirm with your accountant.

• Capital purchases coded GST on Capital
• GST claimed matches the tax invoice
• Finance contracts posted correctly (liability, interest, GST treatment)



6. Review your GST coding

Go to All apps > GST > Overview, open the Run reports ▼ dropdown and select Transactions by Tax Code. Set the period and your accounting method, then scan every line. To fix a wrongly coded transaction, open it, change the code in the GST column and select Save and close - the report updates as you go. The traps we see most often:

Then tie the GST figures to your balance sheet:

• BAS Detail report (Reports > Standard reports) is run on the same method as your GST settings
• GST payable/refundable on the GST report equals the GST Liabilities Payable balance on a balance sheet run on the same method and date
• Exemption details (GST‑free and input‑taxed sales) are correct
• Run Run reports ▼ > GST Amendments - if a previously lodged period has been edited, the difference will flow into this BAS and you should understand why

The ATO’s own BAS and GST tips page is a good reference if you’re unsure about a particular item.

Help article: What to do when BAS amounts look incorrect

7. Balance your payroll

If you have employees, your BAS or IAS reports PAYG withholding at W1 (total salary, wages and other payments) and W2 (amount withheld). With QuickBooks Payroll powered by Employment Hero, every finalised pay run posts a journal using the BAS‑W1 and BAS‑W2 tax codes, so the figures flow into the lodgement automatically. Go to All apps > Payroll > Employees, open the Detailed Activity Report for the period and check:

• Gross wages on the payroll report equal Wages on your Profit & Loss
• PAYG withheld on the payroll report equals the PAYG Withholdings Payable balance on your Balance Sheet, and what you’ve reported through Single Touch Payroll
• Superannuation expense on the P&L and Superannuation Payable on the Balance Sheet both match the payroll report
• The payroll payments in your bank feed are matched to the payroll journals, not recorded as a second wages expense

Be careful not to confuse PAYG withholding with PAYG instalments. Instalments are pre‑payments of your own income tax (the T fields on the BAS), set by the ATO and entered - or downloaded - during the PAYGI step of the lodgement flow.

Help article: Report PAYG Withholding on BAS and IAS

Help article: Set up and manage superannuation (HeroClear and Payday Super)

8. Run the GST AI Agent pre‑file check

Steps 1-7 are the manual review. Before you open the lodgement flow, let the QuickBooks GST AI Agent (BETA^) run a second pass. It compares the income on your Profit & Loss with the net sales on your BAS return for the same period, lists every transaction that causes a difference, and suggests how to resolve each one. It’s particularly good at catching transactions with no GST rate selected, income posted to an expense account, and income lines carrying a payroll tax code.

To open it, go to All apps > GST > Overview, find the open period on the To do tab, select the ▼ next to Prepare BAS and choose Pre‑file check. (You’ll also be offered it inside Prepare BAS via the “Check your return before you file” prompt.) Then:

• If the Agent reports a difference, select Explain this to me to see which values make it up
• For each flagged transaction, select See how to resolve for the AI explanation, then View to open and fix it - usually the GST code or the account
• If a difference is intentional, select Ignore; fixed items move to the Done tab, ignored ones to the Ignored tab
• Re‑run the check until you can explain any remaining difference, then continue to Prepare return

The Agent highlights and suggests - it never changes a transaction or lodges anything on its own. The Pre‑file check option appears on the Overview page once you’ve lodged at least one BAS in QuickBooks. If you work with a bookkeeper or accountant, running it before you hand over the file means fewer queries back and forth.

Help article: Review your BAS return with the GST AI Agent (Beta)

9. Complete the lodgement flow

Back on All apps > GST > Overview, select Prepare BAS (or Prepare IAS) and work through each screen against the reports you’ve just checked:

• GST screen: total sales, total purchases, GST collected and GST paid match your GST reports (G1, G10, G11)
• PAYG withholding screen: total salaries and total tax withheld match the payroll figures from step 7 (W1, W2); tick I have other PAYG withholding to report if you have W3 or W4 amounts
• PAYG instalment screen: instalment amount (or rate and income) matches your ATO notice - tick the adjust box and give a reason if you’re varying it
• Other taxes screen: FBT instalment, luxury car tax, fuel tax credits or WET entered where they apply
• Summary: the net amount payable or refundable is what you expected - if not, go back to the GST reports before you mark anything as lodged

Help article: Lodge your BAS or IAS in QuickBooks Online

10. Lodge, pay and mark as lodged

Check the due date on your activity statement - for quarterly lodgers it’s the 28th of the month after the quarter ends, with an extra two weeks if you lodge online (except for the December quarter). Our BAS due dates guide lists every date for 2026-27, including weekend roll‑overs.

On the Summary screen, select Mark as lodged. This closes the GST period in QuickBooks: any later change to a transaction dated in that period appears on the GST Amendments report and rolls into your next statement, rather than silently altering figures you’ve already reported. Then lodge with the ATO - electronically from QuickBooks if you’ve connected to the ATO, otherwise through ATO online services (using myID) or via your registered agent.

Once you’ve paid, go back to the To do tab and select Record Payment against the lodged statement so your GST and PAYG liability accounts clear. If you can’t pay in full by the due date, contact the ATO before the deadline to set up a payment plan - engaging early protects your compliance history.

• Due date confirmed (including the online concession if it applies)
• Statement marked as lodged in QuickBooks
• Lodged with the ATO and confirmation saved
• Payment made (or payment plan arranged) and recorded against the statement

Help article: Recording a GST payment (BAS payment)

Are you an Accountant or Bookkeeper navigating QuickBooks new Intuit Accountant Suite or QuickBooks Online Accountant? See this article for extra guidance.

Frequently Asked Questions

Need a hand? A QuickBooks ProAdvisor can review your file before you lodge, or explore the GST AI Agent in QuickBooks today.

If you’re an Accountant or Bookkeeper preparing BAS for clients, see our companion guide for accountants and bookkeepers: BAS season for advisors - Books Review, Intuit Accountant Suite and the GST AI Agent.

**Feature availability varies by product. While available in all QuickBooks supported languages, the AI agent’s output will be English only at launch. We recommend you review all outputs carefully. This information is intended to outline our general product direction, but represents no obligation and should not be relied on in making a purchasing decision. Additional terms, conditions and fees may apply. Product offers, features, and functionality are subject to change without notice.

^[Beta] has limited availability and is subject to change. Features may be more broadly available soon.

This article provides general information only and does not constitute tax advice. Figures were checked against ato.gov.au and in‑product steps against the QuickBooks Australia knowledge base in September 2026. Speak to a registered tax or BAS agent about your circumstances.