EU citizen
2010: entered US as F1 student
2014: got married to US spouse, filed first joint tax return
2015: second joint tax return, left US to live&work in Europe
2016/17: life in Europe
2018: entered US on non-resident H1B visa
Question: I know we could file a joint 1040 but can we also both file separate 1040, or would I have non-resident status for tax purposes in that case and have to file 1040-NR (i.e. no standard deduction). The reason I ask is because after five years as F1 student, one can automatically file as resident for tax purposes and I filed 6 years as a student.
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Yes, you can file Married Filing Separately.
Since you have passed the five years not counting days period as a nonresident (2010-2014), starting from January 1, 2015, as long as you stay within the US for more than 183 days or meet the Substantial Presence Test SPT, you are considered as a US resident for tax purposes. Therefore, in 2018, as an H-1B visa, the same rule applies to you. If you pass SPT, you will be a resident in 2018. However, if you did not stay in the US for more than 183 days, your US spouse can file a statement to treat you as a resident. See Nonresident to resident.
As a resident, you can file Married Filing Separately on the Form 1040. You do not have to file the Form 1040NR.
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