Capital Gains Tax on Real Estate: What Most Investors Miss

You close on a property flip for $450,000. After paying off the purchase, rehab costs, and holding expenses, you walk away with $80,000 in profit. Feels good. Then tax season hits, and you owe $18,000 in capital gains tax. That’s a 22.5% haircut on your hard work.

Most real estate investors focus on acquisition price, ARV, and holding costs. They ignore the tax bill until it arrives. That’s a mistake that costs real money. In 2026, with conventional loans at 7.5% and hard money at 12%, your margins are already squeezed. Every dollar lost to avoidable taxes cuts into your bottom line.

Here’s what most investors miss about capital gains tax on real estate—and how to keep more of your money.

Short-Term vs. Long-Term: The 12-Month Cliff

The IRS draws a hard line at 12 months. Hold a property for less than a year, and your profit is taxed as ordinary income. In 2026, that means federal rates from 10% to 37%, plus state tax. For a flipper in California or New York, the combined rate can hit 50%.

Hold for one year and one day, and you qualify for long-term capital gains rates: 0%, 15%, or 20%, depending on your income. For most active investors, that’s 15% federal. You save 12 to 22 percentage points just by waiting one extra day.

Example: You flip a house in 10 months and net $60,000 profit. At a 32% ordinary income rate, you owe $19,200. If you held 60 more days, you’d owe $9,000 at 15%. That’s $10,200 in your pocket instead of the IRS’s.

The 1031 Exchange: Defer, Don’t Eliminate

A 1031 exchange lets you sell a rental property and roll the proceeds into a like-kind property without paying capital gains tax. The tax isn’t forgiven—it’s deferred until you eventually sell without exchanging.

Use a 1031 Exchange Calculator to see the math. Say you sell a duplex for $500,000 with a $200,000 gain. Without an exchange, you owe $30,000 in federal capital gains tax plus depreciation recapture. With an exchange, that $30,000 stays invested in your next property, compounding your returns.

Key rule: You must identify replacement property within 45 days and close within 180 days. Miss the window, and you owe the full tax.

Depreciation Recapture: The Hidden Tax Bomb

Depreciation is a paper loss that reduces your taxable income each year you hold a rental. On a $300,000 property (excluding land value), you can deduct roughly $10,900 per year for 27.5 years. That saves you thousands in annual taxes.

But when you sell, the IRS claws back that depreciation at a 25% rate. This is depreciation recapture. Many investors don’t realize this applies even if you didn’t claim the depreciation. The IRS assumes you took it.

Run numbers through a Depreciation Calculator before you sell. For a property held 10 years with $100,000 in total depreciation, you owe $25,000 in recapture tax on top of capital gains. That can turn a profitable sale into a break-even.

Net Investment Income Tax: The 3.8% Surprise

If your modified adjusted gross income exceeds $200,000 (single) or $250,000 (married), you also pay the 3.8% Net Investment Income Tax on your capital gains. This is separate from regular capital gains tax and depreciation recapture.

On a $100,000 gain, that’s an extra $3,800. Most investors overlook this until their CPA flags it.

The Self-Directed IRA Loophole

Use a self-directed IRA to buy real estate, and all gains grow tax-deferred or tax-free (if using a Roth IRA). No capital gains tax, no depreciation recapture, no NIIT. But you cannot use the property personally, and all expenses must flow through the IRA.

This works best for long-term holds. For flips, profits stay in the IRA until withdrawal, but you avoid immediate tax.

Cost Segregation: Accelerate Depreciation

A cost segregation study separates a property into components (cabinets, flooring, HVAC) with shorter depreciation lives—5, 7, or 15 years instead of 27.5. This front-loads depreciation deductions, reducing taxable income in early years.

When you sell, you still pay recapture, but the time value of money works in your favor. A $10,000 deduction today is worth more than a $10,000 deduction in 20 years.

Primary Residence Exclusion: $250,000/$500,000

If you live in a property for two of the last five years, you can exclude $250,000 of gain (single) or $500,000 (married) from capital gains tax. This is the biggest tax break in real estate.

Convert a flip into your primary residence for two years, and that $80,000 profit becomes tax-free. No 1031 exchange needed, no depreciation recapture, no NIIT. You just need to live there.

State Tax Differences

Nine states have no capital gains tax: Alaska, Florida, Nevada, New Hampshire, South Dakota, Tennessee, Texas, Washington, and Wyoming. If you’re flipping in California (13.3% top rate) or New York (10.9%), state tax can double your total liability. Consider where you hold properties.

Practical Strategy for 2026

With 7.5% conventional rates and 12% hard money, your cash flow is tighter. Every tax dollar saved matters. Here’s a simple checklist before any sale:

Check holding period – Can you wait one more day for long-term rates?
Consider a 1031 exchange – Are you buying another investment property soon?
Plan for recapture – How much depreciation have you claimed?
Estimate NIIT – Will your income trigger the extra 3.8%?
Evaluate state tax – Is it worth moving the sale to a no-tax state?

Use a Capital Gains Tax Calculator to estimate your total liability before you list. Knowing the number changes your decisions.

For rental properties, a Real Estate ROI Calculator or Rental Property ROI helps you model after-tax returns. Tax strategy isn’t just about compliance—it’s about maximizing what you keep.