Undergo conversion in church structure, we hear (5)
I believe the answer is:
alter
'undergo conversion' is the definition.
(to alter is to be changed or converted)
'church structure we hear' is the wordplay.
'church structure' becomes 'altar' (I've seen this in another clue).
'we hear' indicates a 'sounds like' (homophone) clue.
'altar' is a homophone of 'ALTER'.
'in' is the link.
(Other definitions for alter that I've seen before include "reform" , "Change, modify" , "shift" , "Make changes to" , "and 10 Across: Second self" .)