Translation:My house is located inside of a church.
http://www.nytimes.com/2014/06/05/greathomesanddestinations/and-there-was-light.html - Like that, or would it imply a building inside of a building?
My first thought was a building inside of a building. If it's an apartment it isn't too weird, only a bit awkward way to say it, because most people don't think apartment when they hear huis. If you own or rent the whole building, you could say Mijn huis is een kerk.
BTW especially the last 10-20 years it's quite normal for churches to be turned into restaurants, shops, houses (usually apartments if it's a big church), etc, because less and less people in the Netherlands are going to church. But it's not something exclusively of recent years. E.g. Paradiso (a club/music venue that is world famous in the Netherlands) is situated in a church (squatted in 1967, the club opened in 1968). It's often called 'poptempel' for good reason. :)