I reside in Ohio, I have a drivers license there and the company I work for is in Ohio. The company has had me traveling to Illinois for the last 2-3 years. They pay me as if I am in Ohio, additionally I also get lodging and food money back. This last year I decided to rent an apartment. I am not sure how to do my taxes. Do I need to claim the apartment? Do I also need to file in Illinois even thought the company I work for is paying me directly from Ohio to be on-site in Illinois?
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Q. Do I need to claim the apartment?
A. No. As a W-2 employee, you are not allowed(since the 2018 tax law) any business deductions. However, your employer as allowed to reimburse you on a tax free basis. (under an "accountable plan")
Q. Do I also need to file in Illinois even thought the company I work for is paying me directly from Ohio to be on-site in Illinois?
A. Yes, since you physically work in IL. The apartment is irrelevant, you should have been filing an IL non resident return for the last 2-3 years. You also file an Ohio resident return and pay OH tax on all your income, regardless of where earned. OH will give you a credit (or partial credit if IL has a higher tax rate) for the tax you pay to IL.
"They pay me as if I am in Ohio"
That's wrong. You work in Illinois, not in Ohio. It doesn't matter that your employer's headquarters or payroll office is in Ohio. They should be withholding Illinois tax, and box 15 on your W-2 should say IL. If you file your tax returns properly, you will pay most of your tax to Illinois and very little, if any, to Ohio.
If your employer will not withhold Illinois tax, you should be making quarterly estimated tax payments to Illinois.
"additionally I also get lodging and food money back"
How do you get the lodging and food money? Is it a fixed amount, or do you report your actual expenses to your employer? Do you get a separate check for expenses or is it included in your pay?
If the reimbursement is paid through an accountable plan you don't put it on your tax return, and you don't pay tax on it. The plan would have to be established by your employer. An accountable plan would generally require you to submit expense reports with receipts, but that might not be required if the plan meets the requirements for per diem reimbursement. Reimbursement from an accountable plan would not be included in the amount on your W-2.
If the reimbursement is not through an accountable plan, it's just additional pay, no matter what the employer calls it. It should be included in the wages on your W-2 and you pay tax on it the same as any other pay.
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