As an employer, you are not off the hook when it comes to taxes. But, how you pay taxes depends on your business structure. If you are incorporated and receive a salary, payroll and income taxes are deducted from your gross wages. If you are self-employed, you do not receive a salary, but you still need to pay taxes on your income. Instead of FICA tax, you must pay self-employment tax. With self-employment tax, you pay the entire 15.3% for Social Security and Medicare taxes. And, you need to pay income tax. Self-employed individuals pay estimated taxes, which includes both self-employment and income taxes.