The interior is a baroque overflowing with statues of James Bertessi and vault, painted by the artist Antonio Palomino to have it ready on the day of San Juan of 1701.

Luis Lopez, son of the painter Vicente Lopez, made a restoration of the frescoes in 1861.

The altarpiece is the missing church of the Assumption of Betolaza (Alava), which was brought to the church of the Santos Juanes in 1969.