IRS state that commissions must be taxed at a flat 22% rate for fed taxes. Since my overall income is taxed higher rate, will I owe more money at the end of the year?

[Opus 17]

Yes. Withholding is only an estimated pre-payment of tax.  Your actual taxes are calculated at the end of the year and if you owe more than your payments and withholding, you will owe a payment.

[TomD8]

To expand a little on Opus 17's answer, that 22% is the rate at which your employer must withhold taxes on your commission income if he uses the "percentage method."  Your actual taxes may be more or less than that amount.

[Critter]

It should be at a min 22% on a separate commission check ... if your tax rate is higher then the employer should be using that higher rate  if this is added to the same paycheck as the reg wages.  If they give you a separate commission check then you can request they withhold more  OR  adjust your normal withholding so they withhold more from the reg pay to compensate for the underwithholding on the commissions.  It is a tricky balancing act ... discuss this with the payroll dept.

[TomD8]

But if the employer chooses the "percentage method" for withholding on separate commission checks, 22% is the only percentage allowed.  See Section 7, Supplemental Wages, in this IRS reference:  <a rel="nofollow" target="_blank" href="https://www.irs.gov/publications/p15#en_US_2018_publink1000202352">https://www.irs.gov/publications/...>

[Critter]

Then adjusting the other checks or making an estimated payment is the available options.

[EricLind]

What if you're paid straight commission? I earn no salary, no set amount. My pay is 100% commission.