BAS Lodgement Mistakes That Cost Sydney Businesses Time, Cash, and Sleep

Ever noticed how a small BAS hiccup rarely stays small? One wrong GST code or a rushed payroll figure can turn into a cashflow gap, an amended BAS, and a pile of cleanup work you end up doing when you should be running the business. It’s not just penalty risk. It’s the time, the distraction, and the stress of feeling like you’re always catching up.

For Sydney businesses, this happens a lot because the pace is fast and the moving parts add up quickly. You might have a mix of POS sales, online payments, contractors, staff on different pay cycles, and expenses across multiple suppliers and subscriptions.

The business grows, but the bookkeeping process often stays the same. That’s when BAS becomes reactive, and reactive BAS is where mistakes multiply.

Below are five BAS Lodgement in Sydney mistakes that registered agents see over and over, plus the simple controls that stop them from becoming expensive.

1) GST claimed on the wrong things (or missed entirely)

GST mistakes usually come from two places. The first being claiming GST where there isn’t any, or failing to claim GST credits you’re entitled to.

On the over-claim side, it’s common to see GST applied to transactions that are GST-free or don’t carry GST at all. Things like certain fees, wages, and some categories of spending get coded incorrectly, often because someone assumes “expense equals GST” or relies on a default code in the software.

On the under-claim side, businesses miss legitimate credits because bills are coded incorrectly, supplier settings are wrong, or tax invoices aren’t stored properly.

This is especially common when accounts are being updated by multiple people, or when you have a mix of recurring subscriptions and ad hoc supplier invoices.

The damage is rarely limited to one quarter. An incorrect net GST figure often means an amended BAS, a repayment, and a round of evidence gathering you didn’t plan for.

Even when the numbers aren’t huge, the time cost is real: digging up invoices, explaining why a figure changed, and rebuilding confidence in the books.

What to do instead:

• Set clear supplier rules in your accounting software (GST-free, GST included, mixed) and review them quarterly.

• Keep your chart of accounts clean, so it’s harder to miscode items into the wrong bucket.

• Each month, review uncoded transactions and any GST suspense or clearing accounts so issues don’t build until lodgement week.

• Make “tax invoice saved” a non-negotiable step for any GST claim. No invoice, no claim.

2) Cash vs accrual confusion that skews your BAS

This one is more common than people realise. Businesses say they report on a cash basis, then lodge as if they’re on accrual, or they switch methods and don’t adjust the process.

Cash basis generally means GST is reported when money is received or paid. Accrual basis generally means GST is reported when the invoice is issued or received, regardless of payment. If you mix those approaches, you can understate or overstate GST, and your cashflow planning becomes guesswork.

It also creates the worst kind of surprise: you thought you were “fine this quarter” and then the ATO reconciliation doesn’t match your expectation because you’ve pulled forward GST you weren’t meant to report yet, or you’ve delayed GST that should have been declared. Even if you’re not trying to do anything wrong, the outcomes look messy.

What to do instead:

• Confirm your GST reporting method and keep it documented somewhere obvious (not just in someone’s head).

• Align the bookkeeping process to that method. If you’re cash basis, build your checks around payments and receipts, not just invoices.

• Lock the settings and train anyone touching the books, so the method doesn’t drift over time.

• If you change methods, treat it like a real change: check your settings, confirm the effective date, and make sure your reporting matches.

3) Payroll figures that don’t match W1 and W2

W1 and W2 errors often creep in through “little fixes” across payroll and bookkeeping. Manual adjustments, allowances, termination payments, or journals can cause a mismatch between payroll reports and BAS fields.

Sometimes the payroll system is correct, but the BAS report is pulling from the wrong accounts. Other times, someone “cleans up” a wage expense in the ledger and unintentionally breaks the link to the BAS labels.

Super can also become part of the problem when it’s recorded inconsistently or paid late. Even when there’s no ill intent, late super payments can become a compliance headache. And if payroll and bookkeeping aren’t aligned, it’s easy to lose track of what’s been accrued versus what’s been paid.

The practical cost is the time spent reconciling, then reconciling again, then trying to explain why payroll reports don’t match what was lodged. That’s time you don’t get back.

What to do instead:

• Reconcile payroll reports to BAS fields before each lodgement, every time. Don’t assume it “should match.”

• Keep a simple checklist for payroll events (bonuses, terminations, allowances) so they’re handled consistently.

• Set a super calendar and treat SG as fixed cashflow, not “when we can.”

• If you’ve had drift in the past, ask your BAS agent to confirm the mapping between payroll accounts and BAS labels so the reports are pulling from the right place.

  
  

4) Contractor payments without clean ABNs, invoices, or tracking

Sydney businesses use contractors heavily, which is fine, but it needs structure. Problems show up when contractors are paid without proper invoices, ABNs aren’t captured and verified, or payments aren’t tracked consistently. The most

common pattern is “we’ll sort that later,” and later becomes quarter-end stress.

It’s also where classification confusion creeps in. Even if you’re confident someone is a contractor, you still want the paperwork to match the reality: a clean invoice trail, an ABN on file, and clear payment terms.

The risk is not just compliance. It’s operational: if you can’t easily prove what was paid, to whom, and why, you’ll burn time rebuilding the story. That’s when BAS becomes a detective job.

What to do instead:

• Use a contractor onboarding pack: ABN, invoice requirements, payment terms, and insurance if relevant.

• Maintain a single contractor register and update it as you go, not at quarter-end.

• Save invoices as you receive them, linked to the transaction in your accounting system.

• If your business relies on contractors heavily, run a monthly “contractor sweep”: check ABNs are on file, invoices are saved, and anything uncoded is resolved.

  
  

5) Lodging on time with messy books

This is the most common pattern: businesses lodge by the due date, but they lodge before the books are properly reconciled. That’s when “close enough” coding happens, uncoded transactions pile up, and clearing accounts get ignored. The BAS goes out, then the cleanup starts later, usually when it hurts most.

This is also where amended BAS issues are born. If you lodge incomplete data, you’re more likely to find errors later, and then you’re stuck revisiting old quarters while trying to keep the current one under control.

A good BAS should feel boring. Not because it’s unimportant, but because it’s the output of a clean process. If BAS lodgement in Sydney feels stressful every quarter, it’s usually a sign that the close process is missing.

What to do instead:

• Make the BAS the final step, not the starting point.

• Reconcile bank accounts up to the lodgement date.

• Review and clear suspense or clearing accounts.

• Check uncoded transactions and top suppliers for obvious GST errors.

• Lock the period before you lodge, so numbers don’t shift under your feet.

What to lock down before you lodge

If you want to make BAS easier without making bookkeeping heavier, focus on these habits:

• Reconcile first, lodge last: clean bank recs, cleared accounts, period locked.

• GST rules you follow every month: supplier defaults, invoice storage, and quick anomaly checks.

• Payroll matches every quarter: payroll reports reconciled to W1 and W2, super tracked properly.

• Contractor discipline: ABNs verified, invoices saved, register maintained.

One simple way to reduce stress is to treat BAS as a quarterly checkpoint, not a quarterly scramble. If your process is clean, BAS becomes confirmation, not a crisis.

When a quarterly review is worth it for your BAS lodgement in Sydney

A short quarterly review with a registered BAS agent often costs less than the cleanup work you’re already doing. The value is not just “someone lodges it”. It’s having a process that stays clean, catches patterns early, and stops small errors from turning into expensive fixes.

A good BAS agent will spot the repeat issues: the supplier that’s always coded wrong, the account that keeps collecting uncoded transactions, the payroll mapping that doesn’t line up, or the habit of lodging before reconciliations are actually complete. Fixing one or two of those patterns can change the whole experience of BAS.

If you’d like help tightening up your BAS process and getting it right the first time, Absolute Books & BAS can handle your BAS lodgements and keep your bookkeeping on track, quarter after quarter.