Probably yes.  The IRS is required to revoke the exempt status of any 501(c) exempt nonprofit organization, not just charities exempt under section 501(c)(3), if it has not filed a required tax return for three consecutive years.  Those organizations with annual revenue normally under $50,000, and therefore exempt from filing Form 990 or 990-EZ, are now required to file the “electronic postcard” Form 990-N.  (See Ready Reference Page:  “Small Nonprofits Must File E-Postcard to Retain Exemption”) Since churches are not required to file a tax return they will not be affected by this new rule.

Unless your organization is included in a group exemption for the larger group, the IRS will probably send you a notice of automatic revocation after it has not received a return for three years (including the possible extension period).  More than 584,000 organizations have lost their exempt status since 2008,  the first year the IRS was required to revoke exempt status.  The IRS has established a proedure to recover the lost exemption which can include retroactive reinstatement in some cases.  (See Ready Reference Page: "IRS Explains How to Reinstate Automatically Revoked Exempt Status") 

Rev: 10/15