1. Check whether you already have a late fee expense account. Go to Settings, then Chart of accounts, and look for something like "Late Fees," "Finance Charges," or "Bank Charges" under Expenses. Many businesses lump these into a general "Bank Charges" or "Other Expenses" account, which is fine as long as it's consistent.
2. Create the account if it doesn't exist. Select New, choose Expenses as the account type, and pick a detail type like Other Miscellaneous Expense or Bank Charges. Name it clearly so it's easy to find again later.
3. For a late fee in the bank feed (a credit card late fee, for example), categorize it directly. Go to Transactions, then the relevant account, find the fee, and assign it to your late fee expense account, the same confirm-and-add process as any other bank feed transaction.
4. For a late fee added to a vendor bill, add it as its own line. Open the bill, add a line below the original charges, and categorize that line to your late fee expense account rather than lumping it into the same category as the original purchase. Keeping it separate is what lets you actually see how much late fees are costing you over time.
5. Pay the bill as usual. Once the fee is on its own line with the right category, paying the bill works exactly like any other bill payment; the fee just flows to its own expense account on your Profit and Loss instead of getting buried inside another category.