How Do I Catch Up on Months of Overdue Bookkeeping? A Reconciliation Plan, Account by Account

Last updated: 25 October 2026.

If your bookkeeping is months behind, the hard part is rarely the accounting. It is knowing where to start. This guide is the hands-on companion to our plan for catching up on overdue bookkeeping and BAS, which covers penalties, lodgment order and ATO contact. Here we focus on the bookkeeping itself: what to collect, how to get old transactions into your software, the order to reconcile in, how to sort the unknowns, and how to stop the work unravelling.

The examples use Xero because that is what many of our Sydney clients use, and we have checked the Xero steps against Xero Central. The same logic applies in any cloud accounting package.

The short version: list every account and month you are missing, collect the statements, load the oldest data first without overlaps, reconcile one account at a time from the oldest month, park the transactions you cannot identify in a query list, and lock each month once it is checked. Then catch up the BAS in order.

Step 1: Build a gap map before you touch the software

Draw a simple grid with one row per account (every bank account, credit card, loan, PayPal or Stripe-type clearing account, and any account that is used for the business even occasionally) and one column per month. Mark each cell: reconciled, data loaded but not reconciled, or missing. This takes 20 minutes and prevents the two most common catch-up failures: missing an account entirely, and reconciling months out of order.

Add two more columns: the closing balance on the bank statement for each month, and whether a BAS was lodged for that period. You can see lodged activity statements for the last four years in the history tab of your ATO online services for business, under Lodgments then Activity statements. A registered BAS agent can see the same history for a client through the ATO’s agent services.

Step 2: Collect the source documents

WhatWhere it comes fromTip
Bank and credit card statementsOnline banking, or your bank on requestThe ATO describes past bank statements as a great resource for reconstructing records, and notes banks may charge for replacement statements. Download statements as files (not screenshots) where you can.
Sales recordsInvoicing system, point of sale, online store, payment platform reportsReconcile sales reports to the bank deposits, because platforms often pay out net of fees.
Supplier bills and receiptsEmail inbox, supplier portals, phone photos, a shoeboxAsk suppliers to resend tax invoices. For purchases over A$82.50 (including GST) you need a tax invoice to claim the GST credit.
Payroll and super recordsPayroll software, super fund and clearing house statementsAgree wages and super to what actually left the bank.
Loan, lease and asset documentsLender, landlord, finance companyThe ATO’s records-reconstruction guide lists lenders, landlords and finance companies as sources of copies.
Previously lodged BASATO online services history, or your previous bookkeeperYou will compare your rebuilt figures to what was lodged.

If records have been lost, the ATO’s guidance on reconstructing records suggests asking customers and suppliers (who may hold invoices and remittance advices), your bank, lenders, off-site service providers and any cloud data you can retrieve. Keep a note of how each reconstructed figure was worked out. The ATO’s general record-keeping rules say records must show the date, amount and description of each transaction, plus GST information.

Step 3: Load the old transactions without creating duplicates

Connect the bank feed first, then fill in the history that the feed does not cover.

  • Check how far back the feed goes. Xero says that when you first connect a bank feed you can import up to 12 months of history, and up to 2 years with some banks. Look at the earliest date that actually arrived rather than assuming.
  • Import older months from a file. Xero recommends OFX, QFX or QuickBooks files where your bank offers them, and also accepts CSV. For a CSV you only need Date and Amount columns, with income as positive and expenses as negative amounts in the same column. Remove opening and closing balance columns, empty rows and the account number, because Xero works out the balance from the transactions. A CSV is limited to 100,000 rows.
  • Stop the file before the feed starts. Import only the months the feed does not already hold. Overlapping dates create duplicate statement lines that you will then have to untangle.
  • Credit cards use the reverse sign. Xero’s CSV guidance says to show credit card payments as positive and purchases as negative. Check one month before loading the lot.
  • PDF-only statements. Xero says you can upload PDF statements from supported banks. If yours is not supported, you may need to convert the PDF to CSV and check the totals against the statement.

After each import, compare the closing balance in your software with the closing balance on the statement for the last imported day. If they differ, fix the import before you code a single transaction.

Step 4: Reconcile oldest first, one account at a time

Pick one account and work forward from the earliest missing month. Start with the main operating account, because sales receipts and supplier payments usually run through it. Then do the credit cards, then loan and clearing accounts.

  1. Do the easy matches first. Invoices paid by customers, bills paid to suppliers, transfers between your own accounts, loan repayments, payroll runs.
  2. Code the repeaters. Rent, subscriptions, insurance, software and bank fees recur every month. Code the first instance carefully and use your software’s suggestions or rules for the rest, then review the results rather than trusting them blindly.
  3. Check each month-end against the statement. After every month, the book balance should equal the statement closing balance. If it does not, find the difference now, while the month is small, not at the end.
  4. Use the period reconciliation feature if you have one. In Xero you enter the date range and the opening and closing balances from the statement, and you cannot close a period until the balances match and every transaction in it is reconciled. Xero recommends closing periods in chronological order, and once a period is closed you cannot delete or unreconcile its transactions, though you can still edit account codes.

Our guide to how long to keep business records explains what to keep once the work is done.

Step 5: Sort the unknown transactions

Almost every catch-up job has a pile of transactions nobody can identify. Do not guess, and do not leave them inside a generic expense account. Create a query list instead:

  • Park them in a clearly named holding account while you work, so reconciliation can keep moving.
  • Group the queries by payee or by theme, and send the owner one consolidated list (date, amount, payee text), not 80 separate emails.
  • Split genuine mixed-use payments, and keep a note of how the private portion was worked out. The ATO’s record-keeping rules say that where expenses are partly private, you need clear documents showing the business portion.
  • Check the GST on each coded item. The ATO says you need a tax invoice to claim a GST credit on purchases over A$82.50 (including GST). If the supplier does not provide a valid tax invoice within 28 days of your request, there is a process for seeking the ATO’s permission, so do not simply claim the credit.
  • Clear the holding account to zero before you finish. Anything left over is a question you still owe the owner.

Step 6: Manual “mark as reconciled” is a last resort

When a statement line is genuinely missing and cannot be imported, Xero lets you mark an existing transaction as reconciled. Xero’s own guidance says to use this only if you cannot import the original bank statement data, because it creates a new statement line, and if the real line later arrives you end up with a duplicate and a bank balance that no longer matches online banking. Work out why the transaction is missing first.

Step 7: Lock each month once it has been checked

Xero’s lock dates stop users adding or changing transactions dated on or before the lock date, and only administrators can set or change them. Setting a lock date after each reviewed month protects your clean-up from accidental edits, and it makes any later change a deliberate decision. You can remove the lock temporarily if a genuine correction is needed.

Step 8: Prepare the BAS from the clean books

Only when the periods are reconciled should you prepare the activity statements, oldest period first. Two points from the ATO matter during a long catch-up. First, the 4-year time limit for claiming a GST credit runs from the lodgment due date of the BAS for the period in which you could first have claimed it, and the ATO has no discretion to extend it. So older periods with unclaimed credits deserve attention first. Second, cash versus accruals affects which period a purchase belongs in, so confirm your GST accounting method before you code. For the lodgment sequence, penalties and talking to the ATO, follow our catch-up and BAS guide, and keep an eye on the current BAS due dates.

Step 9: Stop it happening again

The ATO’s guidance on when to do record-keeping tasks suggests recording income and expenses as they happen, running a bank reconciliation every month and reviewing your turnover monthly if you are not registered for GST. A monthly close, a recurring reminder and bank feeds covering every account are usually enough to keep a clean set of books clean.

How long will it take?

It depends on the number of accounts, the transactions per month, the state of the records and how quickly the owner answers queries. We do not guess at a duration without seeing the files. We scope the work first, then give a fixed fee for the clean-up in writing.

How we help

We rebuild and reconcile overdue books for Sydney small businesses and not-for-profits, then move you onto a simple monthly routine. See our bookkeeping services and BAS agent services, or email info@guidancegrowth.com.au or use our contact page. A short scoping call, and a fixed fee in writing, is how we start.

Frequently asked questions

Where do I start if my bookkeeping is months behind?

List every account and month you are missing, collect the statements, load the oldest data first, then reconcile one account at a time from the earliest month, checking each month-end balance against the statement.

Should I reconcile oldest month first or newest first?

Oldest first. Each month’s closing balance becomes the next month’s opening balance, so working forward lets you catch an error while it is small. Xero also recommends closing reconciled periods in chronological order.

How far back can a Xero bank feed import history?

Xero says up to 12 months of history when you first connect a feed, and up to 2 years with some banks. Anything older can be imported from statement files, stopping before the feed’s first date to avoid duplicates.

What do I do with transactions I cannot identify?

Park them in a clearly named holding account, send the owner one grouped list to answer, then recode them and clear the holding account to zero. Do not guess or leave them inside a general expense account.

What if I am missing receipts and tax invoices?

Ask suppliers to resend them. The ATO says you need a tax invoice to claim a GST credit on purchases over A$82.50 including GST, and has a process if a supplier does not provide one. Keep a note of how any reconstructed figure was worked out.

Can a bookkeeper catch up the BAS as well?

Only a registered BAS agent (or other registered tax practitioner) can charge to prepare and lodge BAS. You can check any practitioner on the Tax Practitioners Board public register.

Sources and further reading

This article is general information, not personal advice. Rules and dates can change, so check ato.gov.au or acnc.gov.au for the latest, or speak to us about your situation.

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