Currently, we're unable to support corrections to already submitted (by paper or e-file) 1099s. Customers have to complete and submit any corrected 1099-MISC or 1099-NEC outside QBO. That said, you'll have to get in touch directly with the IRS to do a manual amen...
3.2 Check the correction option if you efile 1099 formsez1099 software can prepare, print and efile forms W2G, 1097BTC, 1098s (1098, 1098C, 1098E, 1098F, 1098Q, 1098T), 1099s (1099A, 1099B, 1099C, 1099CAP, 1099DIV, 1099G, 1099INT, 1099K, 1099LTC, 1099MISC, 1099NEC, 1099...
After that, go back to checking your 1099 form and report again. Also, the Nonemployee compensation option has been removed from 1099-MISC. You'll have to choose Box 1 - Nonemployee Compensation on the new 1099-NEC if you filed your 1099-MISC with only Box...
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The IRS has a simple process in place that allows you to amend your tax return. Find out how to amend your tax return in this article on tax tips.