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Yes, you are correct active duty military pay is not taxed in Illinois. See Pub102 Illinois Filing Requirements for Military Personnel for detailed information.
Please ensure that you have entered Illinois in the State that you lived in in the "My Info" section even when you were stationed somewhere else:
Also, make sure that you checked the active-duty military box for the W-2 on the"Do any of these uncommon situations apply to this W-2?" screen right after you enter your W-2.
Furthermore, when you get to your state return double-check that your military pay is entered correctly on the "Military Pay Exclusion" screen for Illinois.
I have done all the steps you recommended. This happens year after year and I don't know why. Its showing I owe IL $1100 and we are getting a CA $600 refund. I have the CA as a non-res return. What am I missing? Is there a way to look at my account and see how it was fixed last year. I had to call and to talk to 2 people for a couple hours last year to get it figured out. Thank you
I notice you mention "we" are getting a CA refund of $600. Is there a spouse? Does the spouse also claim IL as home of record? If yes, the spouse's income is taxable to IL. Here is a link to IL Publication 102 that explains the military tax provisions.
Due to a change in the MSSRA law, as of the 2018 tax year spouses of active duty military may choose to file taxes in their active duty servicemember spouse's home of record, even if they never set foot in that state. The spouse still has the option of filing in their own domiciliary state, if they prefer. The choice is up to the spouse.
So you and your spouse could legally file a joint Illinois return, and not file in California at all. Illinois' income tax rates are much lower than California's.
If your wife chooses to file with you in IL, she could obtain a refund of any CA taxes withheld from her pay, by filing a non-resident CA return showing zero CA income.
https://www.military.com/money/military-spouses-residency-relief-act-mssra
Finally, if the same scenario will hold for this year (2020), and she wants to keep filing in Illinois, she should submit CA Form DE4 to her employer, certifying that she is exempt from CA withholding. Here's a link to that form: https://www.edd.ca.gov/pdf_pub_ctr/de4.pdf
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