Are there any big messes in your house right now? At mine, it’s full-on summer mode—I’ve got all four kids home, and there are messes everywhere. And honestly, that’s exactly how a lot of business owners feel about their QuickBooks: messy, chaotic, and a little overwhelming. So in this, I want to talk about the biggest QuickBooks messes and mistakes I see, especially since I often help clients clean up their QuickBooks files so they can confidently maintain them going forward.
Let’s get into it—the biggest QuickBooks messes I see over and over again. These are consistent mistakes that can really throw things off in your books, but the good news is, they’re totally avoidable once you know what to look for.
The first one has to do with PayPal—and it’s a big one: PayPal creating duplicates.
This is such a common frustration. A lot of business owners use PayPal for business transactions, and yes—linking your PayPal account to QuickBooks is best practice. From a bookkeeping perspective, you should treat PayPal like a bank account. It’s a little quirky, I know—it’s not exactly a traditional bank—but for bookkeeping purposes, it functions like one, and linking it is the right move.
Here’s where people get into trouble: they link PayPal, but they don’t know the correct workflow for recording the movement of money between PayPal and their bank account. And when the workflow isn’t right? That’s when QuickBooks starts duplicating transactions.
I’ve had clients come to me saying, “My income looks double what it should be,” and sure enough, it’s all duplicate deposits showing up in their reports. It’s a tough realization when you discover that what looked like great revenue is actually just duplicate data—especially when you’re making decisions based on that incorrect info.
If you’re in my program, don’t worry—we cover exactly how to avoid this and set up your PayPal workflow correctly so you don’t have to deal with any of this mess.
And hey—if you start to notice any of these issues in your own QuickBooks file, don’t hesitate to reach out. I’d love to help you get it cleaned up.
Let’s move on to the second big mistake I see: not understanding categories.
A lot of business owners are nervous to make a mistake—afraid they’ll “break” something in QuickBooks. But here’s the truth: it’s actually pretty hard to break anything beyond repair. Yes, you can enter things incorrectly, but the great news is that it’s almost always fixable.
Now, some fixes take more time than others, and there are extreme cases that can be a bit painful to clean up. But for most people? You’re doing way better than you think. I’d say at least 90% of the clients I work with are much more on track than they realize—it usually just takes a few simple tweaks to get them fully aligned and confident.
So when it comes to categories, here’s what to look out for.
I’m not necessarily talking about the minor stuff like whether you label something as “office supplies” or “office subscriptions.” Honestly, that kind of detail doesn’t make a huge difference. What does matter is making sure you’re choosing the right type of account for the transaction.
For example, I once helped a client who had linked her bank account into QuickBooks—but then she started categorizing every transaction back to that same bank account. That created a circular loop that gave her no usable information in her reports. It was all just spinning in a circle, showing no actual income or expenses.
Here’s a simple guide to keep in mind:
- If money is coming in, it should be categorized as income.
- If money is going out, it should be categorized as an expense.
There are a few exceptions:
- Owner’s pay is typically recorded as equity.
- Loan payments or money borrowed is a liability.
Getting those big-picture categories right matters way more than obsessing over labels.
Another mistake I see a lot? Inconsistent categorizing.
One month, you might mark a subscription as “office supplies,” and the next month, you call it “marketing.” Over time, that inconsistency makes your reports harder to read and your finances more confusing.
That’s where bank rules come in. They’re a powerful feature inside QuickBooks that helps you keep things consistent. If you’re not familiar with rules or how to set them up, I go through it step-by-step inside my program. It’ll make your bookkeeping so much easier and less stressful.
And speaking of mistakes, the next big one I see is when people link a personal bank account into QuickBooks. Let’s talk about that next.
Let’s talk about something super important: do not link your personal bank account to QuickBooks.
Even if you’ve had business expenses come through that account in the past—don’t do it.
Now, to clarify: I’m not talking about a separate account that you opened just for your business, even if it’s technically in your personal name. That’s different. I’m talking about your family checking account—the one you use for groceries, Netflix, and your kids’ field trips. Trying to link that into QuickBooks and sort out the occasional business expense while deleting the rest? That’s a nightmare waiting to happen.
Not only is it confusing for you, it can cause major issues down the road—especially when it comes to tax prep or financial reports. And we’ll get into that more in just a minute.
Now, if you’ve ever used your personal account for business expenses—don’t panic. It happens, especially when you’re just starting out and don’t have a business account set up yet. Or maybe you’re out running errands and forget your business card, so you use your personal card instead. That’s okay!
There are absolutely ways to add those one-off expenses into QuickBooks properly—without ever needing to link your personal account. But again, don’t link the account itself.
In fact, if you’re an LLC, mixing personal and business finances like that can actually put your legal status at risk. That protection you set up your LLC for? It can be compromised if the IRS or a court sees that your business and personal finances are intertwined.
So do your best to use your business card for business expenses. But if you slip up occasionally? We can handle that—it’s no big deal to enter those individual transactions manually the right way.
Another common mistake I see is more of a mindset block—and that’s being afraid you’re going to mess something up.
I touched on this earlier, but it’s worth repeating: I hear from so many business owners who say, “I’m afraid I’ll break something,” or “I don’t want to screw this up.” So what do they do? They avoid it completely. And that leads us straight into the next issue: not doing your bookkeeping consistently.
Those two problems often go hand in hand—fear leads to avoidance, which leads to falling behind. But here’s what I want you to hear: most people are doing better than they think. Truly. And if you just had a little more clarity and confidence, you’d probably feel totally capable of keeping up with your books.
If that sounds like you, and you want that extra support, this is exactly what we work on inside my program. You don’t have to figure it out alone—I’ll walk you through what to do and help you feel confident doing it.
Okay, last thing for today—and this one is a little more technical but important: don’t use the “register” to reconcile. Use the actual reconciliation tool in QuickBooks.
I know the word “reconcile” sounds intimidating. But really, all it means is this: you’re comparing your bank statement to what’s in QuickBooks and making sure everything matches.
It’s one of the most important steps in bookkeeping. And if you’ve downloaded my free Bookkeeping Checklist, you’ve probably seen it listed there as part of your monthly routine. (If you haven’t grabbed that checklist yet, I’ll drop the link in the show notes—it’s totally free and walks you through six simple steps to stay on top of your books each month.)
Reconciliation helps ensure that the numbers you’re looking at are accurate and complete. Because if your books don’t reflect your actual bank account? Then any reports or insights you’re pulling from QuickBooks are basically useless. So don’t skip that step. And don’t let the word “reconcile” scare you off. It’s a simple check that makes a big difference.
One of the biggest questions we ask in the accounting world is: “Is this data complete?” And what that really means is—does every single transaction on your bank statement show up in QuickBooks?
There are a few exceptions where that might not be the case, and that’s totally okay. For example, if you write physical checks, you might have something called a reconciliation discrepancy—that just means the check hasn’t cleared your bank yet, so it’s not showing in your statement. That’s normal.
But in general, you want to be working with complete and accurate data—and here’s why: QuickBooks can be quirky.
Every now and then, it might duplicate a transaction, miss a whole day, or stop syncing altogether without warning. You may not even realize there’s an issue until you’re months behind. And if you’re not reconciling, those problems can sneak right past you. That’s why reconciliation is such a critical step in the bookkeeping process.
Now, here’s where I see a lot of folks get tripped up…
Some people try to do reconciliation by going into the register view in QuickBooks. You’ll see these little letters like “C” and “R” next to each transaction—standing for “cleared” and “reconciled.” And while you can manually mark each one as reconciled in there, I don’t recommend it. Instead, use the reconciliation tool.
It’s much easier, it walks you through everything step-by-step, and it’s designed to make the whole process smooth and straightforward. So skip the manual work and let QuickBooks guide you through it.
Alright—those are some of the most common mistakes and messes I see when it comes to QuickBooks. I hope this gave you a few things to look out for—or maybe even gave you a little nudge to clean up a few things if you found yourself saying, “Oof… yep, I do that.”
And hey—if you’re still feeling unsure or overwhelmed, or if you’re thinking, I don’t even know what you mean by reconciliation tool, then check out my program.
It’s linked in the show notes and it’s called Get Comfy with QuickBooks. It’s made for business owners like you who want to feel more confident using the program without getting stuck in the weeds. It doesn’t take a ton of time, but it makes a huge difference—and you’ll finally feel like you get QuickBooks.
Thanks so much for tuning in today. I’m so excited to be back and to keep bringing you more simple, helpful content about bookkeeping, QuickBooks, and making the money side of business a lot less stressful.
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