My wife and I are filing jointly but i already completed my federal/state taxes but have not filed yet. Does she log in separate and file married jointly too?

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No. Filing jointly means that you put all of your own income and all of your wife's income on the same tax return. A joint return is one tax return for two people. Log back in to the tax return that you prepared and add your wife's information. In the Personal Info section, make sure that the filing status is married filing jointly.