If you only have time for two Porto churches, I would choose Santa Clara for the gilded interior and São Francisco for the museum and catacombs. Add the others for a particular reason: Clérigos for the tower, Carmo for its tiled side wall, or Capela das Almas while you are already near Bolhão.
Santa Clara: the interior I send people to see
Igreja de Santa Clara is at Largo Primeiro de Dezembro 155, just below the Sé. Its restored gilded carving is extraordinary, and the quiet is part of the visit. Entry is ticketed. The church currently lists daily visits 09:00–13:00 and 14:00–18:00; on Tuesdays and Saturdays it closes to visitors at 17:00 for Mass. Check its official page before you go, because services can change the schedule.
São Francisco: church, museum and catacombs
Igreja de São Francisco is close to the river. The visit includes the church’s gilded interior and a museum route with the catacombs, so allow more time than a quick look inside a parish church. Check the official visitor information for current tickets and access.
For tiles, do not miss these walls
Igreja do Carmo has the famous blue-and-white side facade near Clérigos; you can appreciate it from the street without turning it into another paid interior visit. Capela das Almas, by Bolhão and Rua de Santa Catarina, is the easy add-on when you are already shopping or visiting the market. The facade is the main reason to stop.
Clérigos is about the climb
Clérigos is the choice if you want the tower view and do not mind a narrow stair climb. Check the official ticketing page first. If stairs are not for you, skip the tower; Porto has good viewpoints that do not require a climb.
A sensible walk is Sé, Santa Clara, Clérigos and Carmo, then downhill to São Francisco and the river. It is hilly and takes longer than the line on a map. These are active religious places as well as heritage sites: do not visit during Mass, keep your voice low, and follow the signs about photos and flash.
