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I hold a JD (Juris Doctorate, a doctoral degree in the law), concentration in Tax Law & Corporate law, an MBA (specialization in finance & tax), and BBA from Mercer University's Stetson School of Business and Economics, as well as CFP® and CRPS designations.
No ... likely not ... especially if you are talking about prohibiting certain behavior that on YOUR premises that does not align with YOUR religious activity's beliefs
Practicing your religion, in your way, is protected by the 1st amendment to the Constitution
There ARE certain things that are prohibited by IRS and CAN jeopardize 501(c)(3) status
Under the Internal Revenue Code, all section 501(c)(3) organizations are absolutely prohibited from directly or indirectly participating in, or intervening in, any political campaign on behalf of (or in opposition to) any candidate for elective public office.
Also, voter education or registration activities with evidence of bias that (a) would favor one candidate over another; (b) oppose a candidate in some manner; or (c) have the effect of favoring a candidate or group of candidates, will constitute prohibited participation or intervention
And see this from IRS as well:
The organization must not be organized or operated for the benefit of private interests, and no part of a section 501(c)(3) organization's net earnings may inure to the benefit of any private shareholder or individual. If the organization engages in an excess benefit transaction with a person having substantial influence over the organization, an excise tax may be imposed on the person and any organization managers agreeing to the transaction.
But your ability to practice your religion as you see fit is a constitutionally guaranteed right, and IRS not only will not pursue this area, but could be barred from doing so by federal law
As a mater of fact IRS has been restricted by congress, regarding auditing churches
Congress has imposed special limitations, found in section 7611 of the Internal Revenue Code, on how and when the IRS may conduct civil tax inquiries and examinations of churches. The IRS may begin a church tax inquiry only if an appropriate high-level Treasury official reasonably believes, on the basis of facts and circumstances recorded in writing, that an organization claiming to be a church or convention or association of churches may not qualify for exemption, may be carrying on an unrelated trade or business (within the meaning of IRC § 513), may otherwise be engaged in taxable activities or may have entered into an IRC § 4958 excess benefit transaction with a disqualified person.
So again, 501(c)(3) status as a tax exempt non-profit is threatened only by issues of political activity, benefiting individuals in ways that are in excess of their value to the charity, or carrying on something that is FOR-profit ... How the religious activity is carried out is a protected right.
It IS possible that if you restrict activities ALSO protected by the first amendment, such as OTHERS' rights to practice THEIR religion, or freedom of expression, or assembly ... that this OTHER group may have a constitutional cause of action (ability to sue) your group or leadership, but this wouldn't be an IRS-tax exempt status issue.
And if you are talking about disagreement within the SAME church, this may cause a split, or other acrimony, but would not cause loss of 501(c)(3) status either
Let me know if you have questions