First of all, you're correct. Unlike repairs and general maintenance expenses, a roof replacement needs to be treated as a capital expense and therefore is depreciated over time.
For residential rental properties, the depreciation period is 27.5 years, so if you spent $10,000 on the new roof, you would depreciate about $364 per year, prorated in the first year depending on what month the roof was installed.
If you installed the new roof before the rental property was put into service (rented out for the first time), you can simply add the cost of the roof to the property's cost basis and depreciate it all as one asset. However, in your case it sounds like the property was already being used as a rental, so you'll treat the new roof as a separate asset for depreciation purposes.
How to report the new roof on your tax return
Now, let's get to the actual paperwork part of it -- where do you depreciate the cost of a new roof on your taxes?
Depreciation is reported on IRS Schedule E (line 18 on the 2020 form). But this is the lump sum depreciation you're claiming for all of your rental properties and capital expenses. If you had rental property or assets (like your roof) that were first put into service in 2020, you'll need to also fill out Form 4562, like the IRS told you.
You would list the roof under "residential rental property" on the form (line 19h), listing the month and year your roof was installed and your cost basis in it. In other words, you would treat it just as if you had bought another house and needed to fill out a Form 4562 to report it.
In subsequent tax years, you won't have to fill out the Form 4562 again for the roof -- it's only a requirement in the year the property was put into service.
As a final note, while I sincerely hope you found this helpful, I'd like to point out that I am not a tax attorney, CPA, or other type of tax professional, nor do I have detailed knowledge of your personal tax situation. I'm a real estate investor who knows that particular part of the tax code well, but don't take what I'm saying as a substitute for professional advice. If you're unsure about how to calculate or file any tax item, I strongly suggest consulting with a licensed professional.
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