Bookkeeping clean-up checklist

Hiring a bookkeeper or accountant doesn’t mean you have to have spotless books, but a little cleanup can make a big difference. The tidier your records, the faster your new financial pro can get up to speed — and the less you’ll spend on billable hours. Think of it like tidying the house before the cleaner arrives: You’re not trying to make it perfect, just organized enough so that the expert can do their best work.

In this guide, we’ll walk through how to clean up your bookkeeping before you hand it off, including what to fix, what to gather, and when to stop scrubbing and start delegating.

Cleaning up your books before bringing in a bookkeeping professional saves time, money, and confusion. Even a few small fixes can make your bookkeeper’s work faster and more accurate, giving you a clearer picture of your business along the way. 

Here’s why a pre-clean is a good idea.

1. Save money on bookkeeping hours

Most bookkeepers charge by the hour. If your books are full of uncategorized transactions or duplicates, they’ll need extra time to sort things out. Tidying up now means fewer billable hours spent on detective work and more spent on useful insights.

2. Reduce back-and-forth with your bookkeeper

When your income, expenses, and receipts are easy to follow, your bookkeeper can start right away, instead of pinging you for missing context. It’s the difference between handing them a puzzle with all the pieces versus one with missing corners.

3. Build trust and clarity from day one

A clean set of books shows that you’re organized and serious about your finances. That sets the tone for a professional relationship built on accuracy and transparency.

4. Catch mistakes before they snowball

Taking a close look at your records can surface errors you didn’t realize were there, from double-counted expenses to missing invoices. Fixing these mistakes before handoff helps ensure your accountant’s reports and advice are based on the right numbers.

Before your new bookkeeper can start untangling your books, they’ll need a clear picture of how your business runs and where your financial data lives. 

At a glance, here’s what they’ll want to see:

• Your financial accounts: Grant them view-only access to your business bank and credit card accounts, so they can directly verify transactions.
• Your chart of accounts: Share a list of categories showing how income and expenses are tracked.
• Recent statements and reconciliations: Your bookkeeper will need these to confirm that your books match your account balances.
• Documentation for income and expenses: This includes digital receipts, invoices, and records stored in one place.
• Business context: Compile notes on recurring payments, one-time purchases, or transfers that might need clarification.

Think of this as the pre-work to your bookkeeping clean-up checklist, which we’ll unpack in detail in the next section.

Mercury tip: When you categorize transactions in your Mercury account, it helps your bookkeeper hit the ground running. Clear categories mean fewer follow-up questions and faster bookkeeping setup.

If your books have been collecting digital dust, this is your chance to give them a reset. This bookkeeping clean-up checklist walks you through how to get your books ready for a professional.

1. Organize your income and expense records

Start by gathering all your income and expense data in one place. Pull reports from your accounting software or export CSVs from your bank and credit card accounts. If you’ve tracked your finances in a spreadsheet, make sure every payment, deposit, or refund is logged. The goal is to have a complete record for the period you’re handing off. 

If you’re using a Mercury account, you can manage company expenses in one place — from corporate cards to reimbursements — so every payment is automatically logged, categorized, and ready to review. If you’re not currently using Mercury, but still want to make this step easier, try our free expense reimbursement template.

2. Categorize any uncategorized transactions

Every transaction should have a clear home, whether that’s paying for software, booking travel, or business revenue. Go through any “uncategorized” or “miscellaneous” line items in your books and assign them to the correct category. This is one of the biggest time-savers for your bookkeeper, since it removes the guesswork and back-and-forth. 

In Mercury, you can set custom rules to automatically map transactions to your general ledger (GL) codes. This keeps categories consistent and saves time during month-end close.

3. Reconcile your bank and credit card accounts

Reconciliation is how you confirm that what’s in your books matches what’s in your bank. Review your most recent statements and check that every transaction appears correctly in your records. If you spot discrepancies, flag them for your bookkeeper.

Sync your Mercury account with accounting tools, like QuickBooks, Xero, or NetSuite, to make reconciliation even faster.

4. Flag duplicates or suspicious activity

Duplicates, missing entries, or unexpected charges can skew your numbers. Cleaning these up now means your reports and balances will reflect reality. If you have a Mercury account, the real-time transaction data can help you spot unusual charges quickly and prevent duplicates before they hit your books.

5. Make sure your chart of accounts is logical and clean

Your chart of accounts is the structure that defines how you categorize everything. Think of it as your financial filing system. Over time, it can get cluttered with overlapping or redundant categories. For example, you might have overlapping labels — such as “software subscriptions” and “apps” — that are tracking the same expenses. Take a few minutes to merge or rename confusing categories, so your financial picture is easier to understand.

If you have a Mercury account, you can sync GL codes from your accounting software. This helps to maintain category consistency across all spend, so your chart of accounts stays clean. 

6. Gather receipts and documentation

Bookkeepers love receipts, but more importantly, the IRS requires them for deductible expenses. Collect digital copies of receipts, invoices, or contracts and store them alongside your accounting records. If you’re using Mercury, you can attach notes to transactions or upload supporting files directly, keeping everything in one place.

7. Back up your records

Before you hand anything off, make a secure backup of your bookkeeping files. Whether you’re using cloud-based software or spreadsheets, having your own copy protects you from accidental deletions or software errors. Plus, itmakes transitions smoother if you ever change software providers or bookkeepers. With Mercury, you can export transactions or statements anytime since they’re stored in the cloud.

8. Summarize what’s left unresolved

Even with your best cleanup effort, there may be questions left unanswered, like transactions you’re unsure how to categorize or old balances you haven’t reconciled. Create a short note or spreadsheet listing these items. If you’re in Mercury, you can leave comments on any transaction. This turns unknowns into action items for your bookkeeper to address. 

There’s a point where extra tidying stops being helpful and starts slowing you down. Here are some quick tips. 

Know when your books are good enough

If your income and expenses are categorized, your accounts reconciled, and any major issues flagged, you’ve done your part. Bookkeepers expect a little mess. What matters is that they can follow the story your numbers tell.

Recognize red flags that require a professional

Some issues are best left to an expert, including:

• Accounts unreconciled for several months
• Late payroll or sales tax filings
• Missing or inconsistent historical data
• Improperly recorded loans, investments, or owner draws

These are exactly the kinds of problems bookkeepers and accountants are trained to solve, so flag them and let your pro handle the fix.

Set your bookkeeper up for success

Before you hand things off, create a short onboarding doc that includes:

• How your business earns and spends money
• Access details for your accounting tools or Mercury dashboard (Here’s how to add your bookkeeper to Mercury.)
• Any open questions or discrepancies
• Your goals for the engagement (For example, this could be cleaning up past months, ongoing maintenance, or both.)

This context helps your bookkeeper get started quickly and avoid duplicate work during the first few weeks.

A few hours spent organizing your bookkeeping records now can save days of back-and-forth later, giving your new bookkeeper a clear, confident starting point.

With Mercury, you can streamline this process from the start. Handling your online business banking through a Mercury account keeps your transactions organized and categorized, so your financial data is always ready for review. And, with Mercury’s accounting automations, you can sync all your bills, card transactions, employee expenses, and incoming payments, all from one account.