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Separated spouse filed for SNAP benefits as single. Does this affect ability to file taxes jointly?
The IRS isn't going to care how you filed for benefits - they're effectively the high man on the totem pole.  The agency that administers the SNAP program is the one who might care.  File the 1040 correctly, and then deal with SNAP as you note.  Do deal with SNAP, though; otherwise they might be in trouble if SNAP notices the discrepancy in an audit of their paperwork. Further, SNAP doesn't necessarily care here either.  SNAP defines a household as the people who live together in a house and share expenses; a separated couple who neither shared expenses nor lived together would not be treated as a single household, and thus one or both would separately qualify.  See this Geeks on Finance article or this Federal SNAP page for more details; and ask the state program administrator.  It may well be that this has no impact for him/her.  The details are complicated though, particularly when it comes to joint assets (which may still be joint even if they're otherwise separated), so look it over in detail, and talk to the agency to attempt to correct any issues. Note that depending on the exact circumstances, your friend might have another option other than Married Filing Jointly.  If the following are true: Then she may file as "Head of Household", and her (soon-to-be) ex would file as "Married Filing Separately", unless s/he also has dependents which would separately allow filing as Head of Household.  See the IRS document on Filing Status for more details, and consider consulting a tax advisor, particularly if she qualifies to consult one for free due to lower income.