Amended Return

[MarkHG]

My amended joint return (married) for 2020 shows owing $3100 in Federal taxes, but have previously paid $850 and $3500 in prior returns that were filed for 2020, under married, filing separately.  Will IRS automatically prior amounts already paid for 2020 and issue a Refund? 

[NashayLO]

No, they will not automatically apply those amounts. You will need to apply the amounts that were paid, to your amended return, to get the correct amount owed or refund due. Please see this TurboTax FAQ, for more information, How do I amend Married Filing Separately returns to Married Filing Jointly?

[fanfare]

"Will IRS automatically prior amounts already paid for 2020 and issue a Refund? "

Eventually, but it could be two or three years from now.

Better to file a correct consolidated (Joint) return that show the total amounts both of you paid or were refunded.