MFJ for federal and MFS for IL will save you money. MFJ for IL would tax the FL income and since FL has no tax, there would be no credit. See How do I prepare a joint federal return and separate state.
Filing Status - IL-1040, Individual Income Tax Return states:
- If you file a joint federal return and one spouse is a full-year Illinois resident while the other is a part-year resident or a nonresident (e.g., military personnel), you may choose to file “married filing separately.” Do not recompute any items on your federal return. Instead, you must divide each item of income and deduction shown on your joint federal return between your separate Illinois returns following the Allocation Worksheet in the Form IL-1040 Instructions.
- If you choose to file a joint Illinois return, you must treat both you and your spouse as residents. This election is irrevocable for the tax year. You may be allowed a credit for income tax paid to another state on Schedule CR. For more information, see the Schedule CR Instructions.
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