10 Things I Hate About QuickBooks Online (And What You Should Watch Out For)

Introduction:

QuickBooks Online is one of the most widely used tools for small business accounting—and with good reason. It’s cloud-based, user-friendly, and integrates with countless apps. But as with any software, it’s not without its flaws. In this post, Jon Markee, your Builder CPA, shares his top 10 frustrations with QuickBooks Online that builders and contractors should be aware of.

From broken AI features to hidden security risks, this list isn’t just a rant—it’s a guide to what to watch out for so you can protect your books and your business.

1. Auto-Categorization Is a Mess

QuickBooks has leaned into AI to auto-categorize bank feed transactions—but the results are inconsistent and often wrong.

• Vendors with default expense categories are miscategorized.

• Similar transactions are being booked to different accounts.

Jon had to disable auto-categorization for all his clients to stop the chaos. If you're using it, check your transaction details monthly—your financials may not be as accurate as you think.

2. Duplicate Transactions in the Bank Feed

Even if a transaction already exists in your books, QuickBooks may still suggest adding it again from the bank feed. This creates confusion and can result in duplicate entries—especially if you're not comparing your books to the bank feed closely.

3. Glitchy New Reporting Tool

The new reporting feature is rolling out unevenly and defaults to "Year-to-Date" instead of "Last Month. "Most home builders don’t reconcile daily, so a YTD report rarely gives an accurate picture. The new format also feels incomplete and unpredictable across clients.

4. Pointless Report Insights

QuickBooks tries to help by showing if expenses are higher or lower than last year—but it offers no useful interpretation.

• Rent tripled? That’s nice to know.

• But what should you do about it? No insight is given. It’s just noise if it doesn’t lead to action.

5. Default Chart of Accounts is a Disaster

When new users set up QuickBooks, the chart of accounts is overly complicated or totally irrelevant.

• Many builders end up with 100+ accounts they don’t need.

• Banks reviewing these financials often get confused or dismissive.

There’s no quick fix feature to clean it up, so most builders are stuck with a bloated, messy chart that hurts clarity and credibility.

6. Dangerously Easy Bill Payments

With just one accidental click, Jon nearly sent out a payment he didn’t intend to. QuickBooks aggressively pushes bill payment features, which may be convenient—but they also open the door to costly mistakes and fees. Be cautious if you're managing multiple bills and not ready to pay them immediately.

7. Security Concerns with QuickBooks Online Accounts

This one’s alarming: Jon’s own QuickBooks Checking account was compromised.

• Multiple unauthorized Netflix charges showed up.

• Industry insiders claim offshore employees are accessing customer info. If you don’t check your accounts regularly, you might not notice missing funds until it’s too late.

8. ACH Chargebacks Are a Risk

ACH payments are popular because of lower fees—but now there’s less protection. QuickBooks has reportedly allowed chargebacks on ACHs even after 90 days. Builders could lose an entire draw payment ($50K–$100K) with almost no way to dispute it.

If you're accepting ACH payments through QuickBooks, proceed with extreme caution.

9. Broken 1099 Tool

The 1099 processing tool has long been useful—until this year. QuickBooks implemented AI features that backfired.

• Vendor info was wrong.

• Forms didn't generate as expected. Jon’s team spent hours correcting mistakes that used to take minutes.

10. Ignored Red Flags in Reconciliation and Undeposited Funds

QuickBooks doesn’t alert users to old, uncleared transactions or lingering deposits.

• These issues skew your P&L and balance sheet, even if your bank rec shows zero variance.

• AI could easily flag matching deposits or undeposited fund issues—but it doesn’t. This leaves critical errors hiding in plain sight, especially for Buildertrend users dealing with processing fees and journal entries.

Final Thoughts

QuickBooks Online is still one of Jon’s favorite tools, but it’s far from perfect. The issues above can seriously impact your reporting, cash flow, and even security. Until QuickBooks makes improvements, builders should take precautions:

• Review bank feeds manually.

• Customize your chart of accounts early.

• Check for duplicate or uncleared transactions.

• Be cautious with bill payments and ACH deposits.

QuickBooks might save you time, but only if you use it wisely.For more builder-specific insights, stay tuned or reach out to Jon Markee at MyBuilderCPA.com.