Mountain of Faith features two playable characters, each with three weapon types, but no personalized spell card bombs. Collecting power items results in an increase in "option" satellites around the character (for a total of four), which behave differently according to the character and weapon type. Each characters' options also fire bullets, and either shift position or freeze in place in focus-fire mode.

The scoring system is based on the Faith meter, which has a refillable gauge and a numeric value (minimum 50,000). As long as the gauge is not empty, the player's Faith value doesn't decrease, but the gauge slowly depletes unless the player is defeating enemies or collecting point items. Point items also partially refill the gauge, and Faith items increase the Faith value. The Faith value directly affects the point value of point items and spell card bonuses.