How to Fix Bank Reconciliation Discrepancies in QuickBooks Online

Beginning Balance Is Off? Here’s What to Do

Few things stop a bookkeeping workflow faster than seeing a warning that your beginning balance is off when reconciling a bank or credit card account in QuickBooks Online.

If you’ve ever opened the reconciliation screen and been met with a large warning message, you’re not alone. This is one of the most common reconciliation issues in QuickBooks Online, and it almost always means that something changed after a previous reconciliation was completed.

The good news is that this problem is fixable. Once you understand why it happens and how to resolve it properly, you can restore accurate reconciliations and trust your financial reports again.

This guide walks you through exactly what causes reconciliation discrepancies, how to fix them step by step, and how to prevent them going forward.

Why the Beginning Balance Matters in QuickBooks Reconciliation

Before you start reconciling any bank or credit card account, the opening balance on your statement must match the opening balance shown on the QuickBooks reconciliation screen.

QuickBooks keeps track of this automatically. If the opening balance changes, it triggers a warning because the software assumes that a previously reconciled transaction has been edited, deleted, or altered.

When that happens, QuickBooks can no longer confidently connect your past reconciliations to your current one.

That’s why the warning exists. It’s not just annoying. It’s protecting the integrity of your books.

What Causes the “Beginning Balance Is Off” Warning

If QuickBooks says your beginning balance is off, there is only one root cause:

A transaction that was previously reconciled was changed after the reconciliation was completed.

This can happen if someone:

• Deletes a reconciled transaction
• Changes the amount, date, or bank account on a reconciled transaction
• Imports duplicate transactions and deletes the wrong one
  

Even small changes can break the link between reconciliations.

Step 1: Use QuickBooks’ Built-In Reconciliation Discrepancy Tool

When you see the warning message, QuickBooks usually offers a link that says it can help you fix the issue.

Clicking this option shows you exactly which transaction caused the discrepancy. This is the fastest way to diagnose the problem.

You will then be able to see any transactions that have been changed or deleted.

Make note of these details before taking any action.

Step 2: Recreate the Missing or Deleted Transaction

If the issue was caused by a deleted transaction, the cleanest solution is usually to add it back exactly as it was originally recorded.

Re-enter the transaction using the correct:

• Vendor or payee
• Bank or credit card account
• Original date
• Amount
• Tax treatment
  

Once it’s saved, return to the reconciliation screen.

At this point, QuickBooks may still show the warning, but the transaction should now be available to clear again.

Step 3: Two Ways to Correct the Reconciliation

There are two correct ways to resolve a reconciliation discrepancy, depending on where you are in the timeline.

Option 1: Reconcile Starting From the Last Correct Statement

This is the cleaner approach when possible.

If you know the last statement date that was successfully reconciled, enter that statement ending date and balance again. Then clear the recreated transaction and complete the reconciliation.

This keeps each reconciliation tied cleanly to its correct period.

Option 2: Allow the Transaction to Clear in the Current Reconciliation

If you’ve already moved on and don’t want to redo a prior reconciliation, you can include the missing transaction in the current period’s reconciliation.

This works as long as:

• The transaction exists again in QuickBooks
• The total difference resolves to zero
  

This method is commonly used in cleanup situations and sample files, but it should be applied carefully in real client files.

When Reconciliation Errors Aren’t “Scary” (But Still Need Fixing)

There are situations where reconciliation discrepancies happen intentionally.

For example:

• Cleaning up duplicated transactions
• Correcting errors from bank feed imports
• Fixing incorrectly entered historical transactions
  

In these cases, it’s often best to:

• Have an accountant undo prior reconciliations, or
• Reconcile again starting from the affected statement date
  

What matters most is that the final reconciliations are accurate and that no unexplained differences remain.

How to Prevent Reconciliation Problems Going Forward

One of the best safeguards in QuickBooks Online is closing the books.

Closing the books doesn’t prevent changes entirely, but it does create a warning when someone tries to edit a transaction from a closed period. This extra step often prevents accidental changes that cause reconciliation issues later.

Regular monthly reconciliation, careful review of bank feed duplicates, and avoiding edits to reconciled transactions will save you hours of troubleshooting.

Why Accurate Reconciliations Matter So Much

Bank reconciliation is one of the most important checks in your bookkeeping process.

If reconciliations are off:

• Your cash balance can’t be trusted
• Reports may be misleading
• Decisions are made using inaccurate information
  

Accurate reconciliations allow you to make real-time decisions with confidence, whether that’s adjusting pricing, planning cash flow, or responding to opportunities as they arise.

Helpful Resources

If you want support keeping your books clean and reconciled, these resources can help:

Compare QuickBooks Online Plans

https://www.mycloudbookkeeping.org/quickbooks-plan-comparison

Download the Free Month-End Checklist for Small Business

https://learn.mycloudbookkeeping.org/small-business-month-end-checklist

Book a Free Consultation

https://www.mycloudbookkeeping.org/consultation

If you’re seeing reconciliation warnings and aren’t sure whether you should fix them yourself or bring in help, it’s always better to ask before moving forward. Fixing discrepancies correctly protects your books and gives you confidence in your numbers.

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Hi, Carrie here from My Cloud Bookkeeping. I work with small business owners and entrepreneurs helping them to keep their business finances in order using QuickBooks Online.

Before you reconcile your bank or credit card statement to QuickBooks Online, you should always check that the opening balance in the statement agrees to the opening balance on the QuickBooks Online reconcile page. This is such an important step that if the opening balance has changed, QuickBooks Online creates a big scary warning.

If the opening balance has changed since the last reconciliation, it’s because you’ve changed a reconciled transaction after the reconciliation was completed. After we walk through the steps in this video, I’ll go over some examples where that might be okay, so be sure to stay to the end. And for now, let’s take a look at what to do when you do encounter a difference.

Oh, that scary warning.

Okay, so here we are in our sample company. You may have heard me say before, go to reconcile your favorite way to get there because there are so many. You may have it bookmarked, accounting reconcile. I can’t even get it with this new format. I just tend to pop up here and go straight to reconcile.

Now I’ve opened it up and straight away you can see we have this scary message right here. Your beginning balance is off by 76.98.

Let’s pop right in here. It says we can help you fix it. And this is going to tell you what happened to make this beginning balance be different to what we reconciled last time.

Now, if we pop in here, we can see there was a check that was deleted. And we have the option to view that check.

It was reconciled, as we can see here. It was for $76.98, which was $68 for utilities, $8 for sales tax, and it was to the city water company.

Now, who knows why we deleted this? Perhaps we didn’t mail it. We issued a new one. But there are better ways to do that than to delete something that’s been reconciled.

So what we need to do now is add that check back into the system. I’m just making a quick note of the details.

We pop up here to create an expense. It was the city water company, underneath from the checking account. That was the one we were going to reconcile. I’m putting it back in at the date that it was in initially.

Water utilities. It was 68.12 plus the GST. I think it said maybe it’s HST. Let’s just make sure that the amount goes to the correct 76.98. Yes, that is correct.

So now I’m going to save and close this.

We’ll go back to our reconciliation.

You can see we still have our warning. So now we have two options.

I tend to go for sort of a cleaner option, which is to say what was the last statement ending date. On the 31st of October, in which case I pop in here, I look at my bank statement, I put in the closing balance on that date, and start recording.

Then when I pop in, you can see I’ve entered the check again. I can clear it and there’s zero difference.

But I also want to show you the other way to do this.

So if we close without saving and I want to move on to the November statement reconciliation, I’ll enter in the amount of my November statement and start reconciling from here.

Now if I go from my statement to here, and check off everything, I select all because it’s a sample company, you can see this amount from October, the 76.98 right here.

When we include it in the November reconciliation, then we’re clear. Everything’s fine. We’re reconciled till the end of November.

In order to prevent transactions being changed after you’ve reconciled, you can close the books, which will give you at least a warning before changing anything. I have another video on that.

I did say I would let you know when you’re likely to encounter this error and when it’s not necessarily scary, but still not fun.

If you’re doing a cleanup job that involves deleting transactions that have been entered incorrectly and reconciling the correct ones, this often happens with duplicated transactions. I would recommend either having your accountant undo the prior reconciliations or using the method where you go back into the reconciliation at the previously reconciled date.

That way, you’re only dealing with transactions that were either outstanding when you completed the prior reconciliation or that you’ve corrected.

The bank reconciliation is one of the most important tools you have to ensure your books are in order. If you have old amounts hanging out unreconciled or opening balance errors, it’s important that you properly resolve them or your books will not be accurate and you’ll be making decisions with information that you cannot rely upon.

You can’t grow your business in a healthy and sustainable way if you’re unable to make decisions in real time, such as adjusting your prices or taking advantage of an opportunity that arises.

I hope this has been helpful. Be sure to like, subscribe, click that ring, that little bell, and I’ll see you in the next video. Cheers.

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