QB Issue Resolution:

I really do understand how confusing it can be when you don’t understand where different balances come from in your QuickBooks Online. I know that I was confused by this same thing when I got started with QuickBooks Online. There are a few different reasons why a real life bank account balance could be different from QuickBooks Online’s bank balance.

Timing and outstanding checks:

The relationship between QBO and your bank is a real-time picture. What this means is that your bank balance and the balance in QBO will only match if you don’t have any outstanding checks.
You can think of the QBO balance as the balance that would be in your checkbook register. When you write a check from your checkbook, you deduct it from your register balance even though it hasn’t actually cleared the bank yet. This process causes your register balance to be different from your actual bank balance.
For example, if your bank balance is $1000 but you have an outstanding check for $50, QBO will enter the check in the register causing it to look as though it has already cleared the bank and will reduce your balance by $50, leaving you with a balance in QBO of $950. The bank balance, however, will continue to read $1000 until the outstanding check has cleared.

Downloaded Transactions:

You may have some outstanding transactions in your Downloaded Transactions area that haven’t yet been assigned to an account in your QuickBooks Online.
These Downloaded Transactions will not have been included in the register balance and can also cause a discrepancy between the balance in QBO and your bank balance.
Accepting them into the register will update the balance in QBO.
As long as they remain in the Downloaded Transactions screen they will not affect your QBO balance.

Duplicate transactions:

Transactions can be incorrectly added to the register instead of being matched to a current transaction already there.

Editing or deleting transactions:

Editing or deleting transactions already in your register can cause discrepancies between the bank balance and the balance in QBO.

Credit Card / Liability accounts:

These types of accounts have the opposite accounting affect on your books then bank (or asset) accounts do. Because of this the Bank Balance column for these accounts will normally be negative. What you want to look at is the Balance column and make sure that is correct (positive).

So, there are some perfectly legitimate reasons a bank account balance may not match with QuickBooks Online. However, it sounds as if you may want to take a look at your account’s Register and take a closer look at what’s causing that balance. It almost sounds as if you’ve got “money out” transactions, as opposed to “money in” transactions. Since your QuickBooks Online balance is a sum of all transactions in that account’s register, we’ll want to look at those transactions to be sure that they’re entered correctly. You can click Transactions > Registers and double click the account to view the Register!

Resolution for Issue 'Hi, in the Chart of Accounts view, when there is a negative balance in QuickBooks online (in the Current Account QB Online Balance column), the column next to it (Bank Balance) shows the same figure but as a positive (so no minus sign). Why?' available: Yes (Solved).
Source: Intuit Community forum.

Hi, in the Chart of Accounts view, when there is a negative balance in QuickBooks online (in the Current Account QB Online Balance column), the column next to it (Bank Balance) shows the same figure but as a positive (so no minus sign). Why?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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