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For example if I transfer $ 5,000.00 from my checking to savings a/c on 6/1 these two entries appear in my bank a/c statement -

Checking:   6/1     -5,000.00 Transfer to checking a/c YYY
Saving:     6/1     +5,000.00 Transfer from checking a/c XXX

Once I import both of these account statements into GnuCash these transactions are marked as imbalanced and with second entry appearing in Imbalance-USD account.

If I go and 'fix' these in Imbalance-USD account, it ends up creating duplicate entries into the other account:

Checking:  6/1    -5,000.00 Transfer to checking a/c YYY
Checking:  6/1    -5,000.00 Transfer from checking a/c XXX

Saving:*  6/1     +5,000.00 Transfer from checking a/c XXX
Saving:*  6/1     +5,000.00 Transfer to checking a/c YYY

To fix it, I now have to go in and delete one of the original transactions:

Checking:  6/1     -5,000.00 Transfer to checking a/c YYY
Saving:    6/1     +5,000.00 Transfer to checking a/c YYY

This process is kind of ok, except that it's a bit too onerous.

It get's even worse when recording credit card payments, since I prefer to maintain proper descriptions on my checking and credit card transactions.

Is there a better way of doing this? Possibly a way to map two existing transactions in GnuCash to resolve this break?

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I'm not familiar with GnuCash matching process, but in your flow - you shouldn't fix both the unmatched transactions. You should only fix one, and manually delete the other. This way you'll get a single transaction corresponding to the actual situation on your accounts.

You should check the GnuCash matching settings, and maybe upgrade to a newer version, it may be a simple configuration/bug-fix issue.

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I think the confusion is that you conflated the two accounts as if they're the same then expanded the transfer to two transactions. You said "These two entries appear on my bank account statement" then you list transactions into two different accounts. My banks would list those two transactions on two SEPARATE statements. HOWEVER, even if they appear on the same bank statement, they must be considered separate asset accounts.

In GnuCash you would create two separate asset accounts such as Checking and Savings. You might also have Cash in Wallet to indicate the currency you're carrying around. Credit cards need their own separate Liability account (NOT an asset since when you use a credit card you increase your debt).

Open the account for Checking to view and record checks and Debit card transactions. Open the Savings account register to view deposits and withdrawals in that account. Open the Credit Card account to see each separate expenditure for the credit card.

A withdrawal of $10 from Savings might create a single transfer to the "Cash in Wallet" account, and then at the bakery you might spend some fraction of your holdings from the Cash in Wallet account.

A transfer of $10 from Savings to checking would be represented by a single transaction. You can open the Savings register and indicate the Checking account, and then a decrease (right column) of $10 in the Savings register.

If you then open the Checking account register, you will see that SAME single transaction, but the columns are switched -- the transfer will appear in the left column to indicate the transfer increases the asset account.

When you purchase something with a credit card, create a separate transaction, so for example if you pay for a meal for $10 you would enter the name of the establishment, the account might be Expenses:Dining and the right column would be $10.

When it's time to pay the credit card bill, you could write a check (or initiate a direct bank transfer). The single transaction in your Checking account might indicate the check number, the date, the name of the credit card company, the account "Liabilities:Credit Cards:Card Name" and the payment amount in the right column, decreasing your asset. When you open your Credit Card register in GnuCash you will see that SAME transaction in the Credit Card register with the payment amount in the left column, decreasing your liability (amount you owe).

If you see any numbers in the imbalance account it means the amounts aren't applied to an appropriate transfer account. In your example, it's because you're trying to represent each transaction in GnuCash with two transactions instead of one.

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