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Your 1099 shouldn't be affected as long as the tracking is correct. Let's find those missing 1099 payments and put them back in the 1099 Transaction report.
The first thing you need to do is check if payments to these vendors meet the threshold. Only those contractors you paid above the annual $600 cash threshold get a 1099.
You can see which contractors didn’t meet the threshold with these steps and the 1099 reports.
If this is a 1099 Vendor using 1099 Accounts, you need to enter more transactions or change the thresholds. Please follow the steps I've outlined below.
If contractors are still missing or amounts are wrong when preparing 1099s, you can use this article: Fix missing contractors or wrong amounts on 1099s.
If you're ready to file your 1099s, check out these articles as guidance for submitting tax returns.
You can always post here in QuickBooks Community if you have other concerns or inquiries about 1099s. I'm always here to make sure that everything is taken care of. May you have a wonderful day ahead!