We'vebeen downtown a few times and recently explored the insides of another historic church. Cuenca is a city of 52 churches... and this one is one is the oldest.
This one was built on Inca ruins. The foundation is from the Inca era. Inside one of the rooms, you can see a cut-out on the floor, looking down to more Inca rockwork.
We paid a nominal fee (I think about $4 for the two of us) for entry and self-tour. The fee goes for ongoing renovation.
The statues are life-size. Very cool.