I am an assistant to a priest at a Church in Massachusetts, and in our Church, we have four bedrooms in an upstairs apartment. We don't make tenants sign leases since they are recently out of college or are having financial troubles. This church is not zoned for apartments or as living quarters. It's legally only a place of worship. The problem is, one tenant is a nightmare. He does his best to sabotage one of the other, lovely, roommates, and treats the priest with the utmost disrespect. He's ruined our newly refinished floors to spite us, broken the rules the father set for religious reasons, lent out and used items belonging to the church [and never retrieved them], refused to pay over $190 for his roommate's groceries and medications he ruined when he left the refrigerator door open all [85 degree] day. I don't know how to force him to leave? I am afraid he's going to harm the building or someone if I evict him, but I can't go through legal protocols because the building isn't zoned for it. How do I evict him?

This question is like the drug dealer asking how to get his buyer to pay the agreed-upon price for drugs. If you can't go to court because you have violated the law in renting the place, there is nothing you can legally do, other than giving him a notice to quit and pray he doesn't call your bluff and force you to take him to court for an eviction order. If you do have to court, it could be that the zoning problem won't be brought up.
I have to say, this is a disappointing situation you and your priest have gotten yourselves in. You, and your church, should be setting an example.
By the way, are you sure the zoning doesn't allow the residential use as incidental to the use as a church?

Agree. It was naïve and foolish not to have a controlled setting for this kind of temporary housing, with a watchful monitor and strict rules. I would hope that the other 3 people could keep such a close eye on the place that he would give up and leave. But really, there's liability in the event he commits arson or harms another person there. Your insurance would be denied, you would be criminally charged, and so on. So you need to kick everyone out, somehow, ASAP. Then apply to zoning for a variance and do it right.

(And right out of college? Give me a break. If you are going to be secret, be a safe house for battered women.)

By the way, the part about not making them sign leases doesn't make any sense. Just because they don't have good credit (I guess that's what you're saying.) doesn't in any way prevent you from asking for a lease. You don't because you choose not to.

I'm sure one of the parishioners is a lawyer. So I suggest you enlist their services in trying to resolve this issue. Does the tenant know this is an "illegal" apartment?

Maybe we are all piling on, but I would offer one other bit of advice. Assuming tha the legality of having residents living on church property is resolved, in order to live there they should definitely be signing an agreement that defines the rules and expectations, and that makes clear that violation of those rules may lead to expulsion. It should be structured like rules that students must abide by when living in a dormitory at college - you can get kicked out immediately for violating school rules, violating the law, etc and the school does not have to go through the standard eviction process like landlords do.

By the way, are you sure the zoning doesn't allow the residential use as incidental to the use as a church?

**Please know that I am a layman and I am not giving legal advice, but asking a question that I hope will add to the answer of this question.**

My church growing up offered temporary housing to the homeless. Those who stayed signed up on a waiting list and volunteers would stay overnight with the people to make sure no one got out of hand. If someone did get out of hand, we could call the police and the rowdy person would be escorted from the property.

Since this was a church service and not an actual residence, the people who stayed didn't sign any contract or lease. I'm wondering if the asker of this question might have some legitimacy, as a church, for offering "relief" housing to the needy?

Since I was young when I was a part of this church, I can't really say if the church signed up with the township in order to legitimately offer this service.

You still file for eviction in housing court. That is the only way to evict them.

This person may or may not bring up that it is a illegal apartment, But being illegal rental does not stop you evicting them, it merely allows them to report you to zoning and code enforcement.

And of course again the church and the dioscese has or should have a dozen attorneys who are paid to handle this sort of things.