Yes. Housing allowance is always included in your total earnings for Self-Employment Contributions Act (SECA) purposes. Therefore, ministers will pay the additional 0.9% tax on the amount of their earnings above the threshold, including the value of the housing allowance. If you reach the threshold through a combination of SECA and FICA earnings, you'll need to compute your withholding on the total amount using calculations in the regulations, which can be complicated. As always, it's important to speak to a professional tax advisor on this and all tax issues.