In favour, fat heretic's prayer (3,6)
I believe the answer is:
our father
'prayer' is the definition.
(I've seen this before)
'in favour fat heretic's' is the wordplay.
'in' indicates a hidden word.
'OUR FATHER' is hidden within 'favour fat heretics'.
(Other definitions for our father that I've seen before include "head of family" , "Early bit of devotion" , "God" , "Lord's Prayer" , "Pater noster" .)