I must admit that I'm not really one for church tourism, and doubly so for church museums. But the visit to the Sacro Iglesia de San Juan is worth it to see the Las Calderonas Altar area. It's a corner of the church that has a gorgeous Gothic style dome and a nice series of wood-panel painting featuring St. John the Baptist, among others. At the end of the altar area, there's a mausoleum-like sculpture of a reclining man that's lit by a solitary window whose light guides the visitor. It looks like something out of Indiana Jones! The rest of the museum shows off nice, if a tad boring, relics from the early church and things like paintings and tapestries.
Another highlight is the choir area; it's nothing out of this world but it's a nice quiet place to sit for a minute and take in the museum's vaulted ceilings and various altar areas all in one glance. Plus, the ancient organ is pretty cool, too.