How CPAs Work with Small Businesses in QuickBooks – And Where Bookkeepers Fill the Gaps

Certified Public Accountants (CPAs) play a crucial role in helping small businesses maintain financial health, ensure tax compliance, and make strategic decisions. However, many small business owners are unsure about what exactly a CPA does (and doesn’t do) in QuickBooks—and where an independent bookkeeper can provide additional support.

In this blog, we’ll explore:

• What a CPA typically does in QuickBooks for small businesses

• What a CPA usually doesn’t handle in day-to-day bookkeeping

• Key areas where an independent bookkeeper adds value

By the end, you’ll have a clearer understanding of how CPAs and bookkeepers complement each other in managing your business finances.

What a CPA Will Do in QuickBooks for Small Businesses

CPAs are licensed professionals who specialize in accounting, tax strategy, and financial compliance. When working with QuickBooks, their involvement is often high-level and focused on accuracy, tax optimization, and financial reporting. Here’s what they typically do:

Reviewing and Correcting Financial Records

• CPAs examine bookkeeping entries to ensure compliance with accounting standards.

• They may make adjustments for tax purposes such as reclassifying expenses or making depreciation entries.

• They work with business owners to verify that financial statements accurately reflect the business’s financial position.

Tax Preparation & Filing

• CPAs ensure that all income, deductions, and credits are correctly recorded in QuickBooks for tax filing.

• They handle complex tax issues like multi-state filings, R&D credits, or 1099 compliance.

• They may provide tax planning advice to minimize liabilities.

Financial Analysis & Strategic Advice

• CPAs analyze financial trends, cash flow, and profitability.

• They may advise on business structure (LLC vs. S-Corp), financing, or growth strategies.

• They help with audits or IRS correspondence.

Setting Up or Optimizing QuickBooks

• Some CPAs assist in initial QuickBooks setup, chart of accounts structuring, and integrating tax-related features.

• They may recommend best practices for categorizing transactions to simplify tax filing.

What a CPA Typically Doesn’t Do

While CPAs are invaluable for tax and compliance matters, they usually don’t handle day-to-day bookkeeping tasks. Here’s what they typically won’t do:

Daily Transaction Entry & Categorization

• CPAs generally don’t record daily sales, expenses, or bank transactions.

• They expect the books to be maintained regularly but won’t do data entry themselves.

Accounts Payable & Receivable Management

• They don’t usually process invoices, send payment reminders, or manage vendor bills.

• Late payments or unpaid invoices are typically outside their scope.

Payroll Processing

• While CPAs can advise on payroll tax compliance, they rarely run payroll or input employee hours into QuickBooks.

• They may review payroll reports but won’t handle weekly/biweekly processing.

Bank & Credit Card Reconciliation

• Reconciling accounts monthly is a bookkeeping task, not typically handled by CPAs.

• They may spot-check reconciliations but won’t perform them routinely.

Fixing Messy Books

• If your QuickBooks is disorganized, a CPA may charge a premium to clean it up—or refer you to a bookkeeper.

• They prefer working with well-maintained records rather than fixing errors.

• Some CPAs will actually refuse to file taxes for you unless you maintain clean books. It is often not worth their time to spend many hours doing clean-up when they would rather focus on tax strategizing. 

Where an Independent Bookkeeper Fills the Gaps

Since CPAs focus on high-level financial oversight, small businesses can benefit substantially from hiring an independent bookkeeper to handle the operational side of QuickBooks. Here’s how a bookkeeper complements a CPA’s work:

Keeping Day-to-Day Books Accurate & Up-to-Date

• Bookkeepers enter transactions, categorize expenses, and reconcile accounts regularly.

• This ensures CPAs have clean, real-time data for tax filings and financial reviews.

Managing Cash Flow & Payables/Receivables

• Bookkeepers track unpaid invoices, follow up on receivables, and schedule vendor payments. They also help avoid cash flow crunches by monitoring account balances. This helps avoid unnecessary fees and penalties. 

Handling Payroll & Employee Expenses

• Bookkeepers process payroll, track PTO, and ensure tax withholdings are correct. They also may manage contractor payments and year-end W-2/1099 filings.

• Bookkeepers can also alert you to employee expenses that fall outside of approved parameters, thus preventing fraud and misuse of company funds. 

Cleaning Up Your QuickBooks

• If your books are a mess, bookkeepers can reorganize accounts, fix misclassified transactions, and set up automation. This saves the CPA time (and the business money) during tax season. Once the books are clean though, the job isn’t done. Without maintenance, the books will fall into bad shape over time. A good bookkeeper can make sure that they stay organized going forward. 

• Even if you’ve hired a CPA to do your tax filing, don’t assume that they will clean up your books. Often times CPAs will just make the adjustments needed in their systems in order to file your taxes, but not update your books to match. The changes they’ve made may not be reflected in the books.

• CPAs are usually more interested in the catalouging tax-related financial activity from the past year than in correcting long standing issues with your books. If your books show unpaid invoices that are years old, or open credit memos from way back, or your chart of accounts is a sprawling mess, these are issues that most CPAs won’t address in their work.

Generating Financial Reports

• While CPAs analyze reports such as P&L statements, balance sheets, and cash flow reports, bookkeepers prepare the reports. It is important to have someone who can prepare these reports correctly, as any mistakes can lead to a misleading analysis by the CPA. 

• Regular reports also help business owners make informed operational decisions.

Providing QuickBooks Training & Support

• Bookkeepers often train business owners or staff on using QuickBooks efficiently.

• They troubleshoot issues like bank feeds not syncing or user access problems.

• A QuickBooks Certified ProAdvisor (such as myself) is a specialist in QuickBooks software. We can therefore act a bit as tech support by guiding you in implementation of the software in a customized manner.  

CPA + Bookkeeper = A Strong Financial Team

The best financial strategy for a small business often involves both a CPA and a bookkeeper:

• The Bookkeeper keeps daily finances running smoothly, ensuring data is accurate and up-to-date.

• The CPA leverages that clean data to file taxes, optimize deductions, and provide strategic advice.

Without a bookkeeper, a CPA may spend costly hours fixing basic bookkeeping errors. Without a CPA, a business might miss tax-saving opportunities or compliance risks.

When to Hire Each Professional

• Hire a Bookkeeper If:

• You’re falling behind on transaction entries or reconciliations.

• You need help with invoicing, payroll, or cash flow tracking.

• Your books are disorganized, making tax time stressful.

• Hire a CPA If:

• You need tax planning, filing, or audit support.

• You’re making big financial decisions (loans, expansions, entity changes).

• You want strategic financial advice beyond data entry.

Final Thoughts

CPAs are essential for tax compliance and financial strategy, but they’re not typically involved in daily QuickBooks upkeep. An independent bookkeeper fills that gap by managing transactions, reconciliations, payroll, and reporting—freeing up the CPA to focus on higher-value tasks.

For small businesses, the ideal approach is to have both professionals working together:

• The bookkeeper ensures accurate, real-time records.

• The CPA uses those records to maximize tax efficiency and financial growth.

By understanding these roles, you can build a stronger financial team—and keep your business running smoothly year-round.

Want to find out more about how I as a bookkeeper can work with your accountant to benefit your small business? Just click here for more information.