In the 17th century the Dutch Republic was a bit of an exception in Europe. We were a Republic amongst monarchies, and also tolerance was something that was treasured.
Since the war against Spain (1568-1648), Calvinism was the main religion in the Netherlands, but other religions were allowed to practice their faith. As long as they did so in silence. Especially the Roman Catholics had to be a bit careful. They could have churches, and the whole town knew a Roman Catholic church was there, but as long as it was not recognizable as a church and they did not do anything in public, they were tolerated.
Some of these Schuilkerken (hidden churches) can still be seen in Amsterdam.
One of the most beautiful churches is called 'The parrot', in the middle of the busy shopping street The Kalverstraat. Inside is a lovely church full of atmosphere. Worth a visit!
Another well known hidden church is at the Begijnhof. The church on the Begijnhof is now an Anglican church, but on the other side you can see this house, with a Roman Catholic church inside. Quite lovely.
An amazing church and also a museum is called Ons lieve Heer op Solder (our dear Lord in the Attic). This beautiful house on one of the famous Canals was bought in the 17th century by a merchant who converted his attic into a Roman Catholic Church. It is still in working order and a Mass is celebrated there every month. The building is now a museum, and I can really recommend a visit if you are in Amsterdam. If you are not afraid of climbing stairs, that is!