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It appears the marketplace subsidies are calculated based on Modified Adjusted Gross Income (check this link at healthcare.gov). That being the case, the clergy housing allowance would not be factored in when determining eligibility for a subsidy.

Dan Busby is president of the Evangelical Council for Financial Accountability (ECFA)—an accreditation organization that sets standards for governance, financial management, and fundraising/stewardship for churches and other nonprofits across the country.