How do duplicate transactions get into bookkeeping software?

The usual path is two entry routes for one event: a bill payment or expense keyed by hand, plus the same transaction imported from the bank feed and added instead of matched. Reconnecting a bank feed can also re-import weeks of history wholesale. Each duplicate doubles an expense or a deposit in the reports.

What is the safest way to delete duplicate transactions?

Reconcile first, then delete the copy that is not reconciled and not linked to anything. Keep the transaction that cleared the bank reconciliation; remove the manual twin — but if the manual twin is a bill payment or invoice payment, unlink or reverse it through the AR/AP module rather than deleting, so customer and vendor balances stay right.

Do duplicate expenses affect my taxes?

Yes. Duplicated expenses overstate deductions and understate profit, which understates tax — an error the IRS treats as yours to fix regardless of software. Duplicated deposits do the reverse, overstating income. If duplicates sit in a year already filed, quantify them and talk to the preparer about whether an amended return is warranted.

Duplicate transactions: when the bank feed and manual entry both count

Symptom

Expenses look roughly double what the business actually spends in certain categories. The bank reconciliation shows a stubborn difference, and the register shows pairs: same payee, same amount, a day or two apart — one from the feed, one keyed by hand. Book cash may have gone negative from the weight of it (/bookkeeping/cleanups-fixes/negative-cash-balance-fix).

Why it happens

Modern ledgers have two front doors. Transactions arrive from the bank feed, and they also get entered by people — bills paid, checks written, expenses logged from receipts. The software tries to match feed items to existing entries, but the match fails when dates differ by a few days, amounts differ by pennies, or the payee string from the bank ("SQ *COFFEE 4821") doesn't resemble the entry ("Corner Coffee"). An unmatched feed item gets "added" as new, and now the event exists twice. The industrial-scale version: a feed disconnects and gets reconnected with an overlapping import window, re-adding weeks of history in one afternoon.

The fix

Reconcile the account first. The reconciliation identifies which copy of each pair actually cleared the bank — that copy is the keeper. Deleting before reconciling risks removing the cleared one.
List the suspects. Sort the register by amount; duplicates cluster. Some platforms report "possible duplicates" directly. Confirm each pair by payee, amount, and proximity of dates.
Check what each copy is connected to. A raw feed expense with no links is safe to delete. A bill payment, invoice payment, or transfer is load-bearing: it holds vendor balances, customer balances, or a second account's register in place.
Remove the unlinked copy. Where the manual copy is the linked one and the feed copy the orphan, delete the feed copy and match the feed line to the manual entry instead. Where the manual copy is an unlinked duplicate, delete it. Never leave a "fixed" pair by changing one copy's amount to zero — that leaves a ghost.
Handle linked duplicates through their module. A duplicated bill payment gets unapplied and deleted in AP so the bill reopens correctly; deleting it from the register orphan-strands the bill. The AR twin of this problem produces negative customer balances — see /bookkeeping/cleanups-fixes/negative-accounts-receivable.
Re-run the reconciliation and confirm the difference is zero. Then check the P&L for the categories that looked doubled; they should drop to plausible.

No journal entry is normally needed — deletion and matching do the work. The exception is a duplicate in a locked period, corrected in the open period instead:

Journal entry — Reversing a duplicated expense locked in a closed period

Account	Debit	Credit
Checking account	740
Repairs & maintenance expense		740

Posts in the current open period to offset a duplicate the closing date protects; document the reference number of the duplicate it reverses.

How to prevent it

Match, never add, in the feed. Train everyone who touches the feed: search for an existing entry first; "add" is the last resort, not the default.
One entry route per transaction type. Decide which things are keyed (bills, payroll) and which come from the feed (card charges), and hold the line.
Check the import window on every feed reconnect before confirming — overlap is where mass duplication is born.
Watch category run-rates monthly. A category at twice its normal level is the earliest duplicate alarm; a whole file full of them is a cleanup engagement (/bookkeeping/cleanups-fixes/books-cleanup-playbook).