How to Use Level Copilot for Bookkeeping Clean-Ups

Bookkeeping clean-ups can feel overwhelming—especially when you’re walking into a file that hasn’t been touched in months (or years). Whether you're onboarding a new client or diving into a neglected set of books, Level can help you hit the ground running.

Our automated error detection software for QuickBooks Online surfaces the most common issues and gives you a prioritized path to resolution. Here’s how to use Level’s built-in reports and rules to tackle your next clean-up project with clarity and speed.

Start with Transaction Volume by User

Before diving into the mess, get a sense of who’s been doing the bookkeeping—and how much.

The Transaction Volume by User report gives you a breakdown of activity by user over time. This helps you:

• Identify whether the file’s been touched recently

• Spot high-activity periods (useful if you’re wondering when things went off track)

• Focus your review on the most active contributors to assess consistency and accuracy

Keep an eye out for transactions posted by “System Administration.” These are automated entries created by QuickBooks Online—often the result of bank feed activity, recurring transactions, or app integrations. They’re not always wrong, but they can lead to duplicate entries or uncategorized transactions if not reviewed properly.

Pro Tip: If you see sudden spikes in volume from a new user (or lots of System Admin entries), zoom in on that period to trace issues to their source.

Review Aged Uncleared Transactions

Next, pull up the Aged Uncleared Bank and Credit Card Transactions report.

These are deposits or expenses sitting in the bank feed for months (or years) without being matched or deleted. Left unaddressed, they throw off your cash balances and can hide duplicate entries.

During clean-ups, this report helps you:

• Quickly see how far back issues go

• Decide whether to match, delete, or investigate aged items

• Communicate with your client about outdated or incorrectly entered transactions

Check for Aged Unreconciled Transactions

Unreconciled transactions are like open wounds in a QBO file.

The Aged Unreconciled Bank and Credit Card Transactions report shows transactions that should’ve cleared the bank but didn’t get marked as such in QBO. This often points to:

• Reconciliation errors

• Duplicates

• Manual entries that don’t match the bank feed

Use this report to clean up bank and credit card accounts and ensure beginning balances line up with statements.

Scan for Problematic Journal Entries

During a clean-up, journal entries are always worth a look—especially if you’re seeing strange balances or misclassifications.

Level flags journal entries that:

• Were used to bypass normal workflows

• Post to accounts that shouldn’t receive journal entries (e.g., bank or AR accounts)

• Are dated oddly or backdated

Reviewing these entries can help you undo band-aid fixes and get to the root of the problem.

Identify Uncategorized or Miscellaneous Transactions

No clean-up is complete without dealing with the dreaded “Uncategorized Expense,” “Ask My Accountant,” or “Miscellaneous” accounts.

Level’s Transactions Posted to Uncategorized, Miscellaneous, or Other Selected Accounts report brings these all into one place. Use it to:

• Reclassify transactions to proper expense/income categories

• Spot vendor transactions that need mapping rules

• Catch lazy or rushed data entry

Cleaning up these accounts helps clients get accurate reporting—and helps you sleep at night.

Tackle Negative Customer Balances

Finally, check the Customers with Negative Balances report.

These balances can come from:

• Overapplied payments

• Misapplied credits

• Refunds that never got recorded

Resolving these issues prevents incorrect AR reporting and helps keep client relationships smooth. It also ensures you're not misstating income or sales tax liability.

Clean-Up Work That Feels Like Progress

Using Level for clean-ups isn’t just about catching errors—it’s about giving you a repeatable, high-confidence workflow for untangling messy books.

Each report gets you closer to a clean file without the guesswork. And since Level runs every day, you can keep an eye on ongoing issues even after the clean-up is done.

Ready to streamline your next project? Start your free trial and let Level do the heavy lifting.