Yes, in Haarlem you'll find a protestant church St.Bavo in the centre (at the market), which houses the Muller organ (which is a property of the city, not the church).
Then you'll find a RomanCatholic cathedral basilica of St.Bavo at the canal (somewhat out of the centre) build in the 20th century, which houses the Adema organ (which came from Amsterdam)
Confusing indeed: the protestant did away with Saints and many other 'catholic' things, but keep names related to churches (Grote- of St. Bavokerk) and sundays (like 'sunday Jubilate' - referring to the old gregorian introitus, which they don't sing).