A footnote at end of service in part of church (4)
I believe the answer is:
apse
'part of church' is the definition.
('apse' is part of 'church')
'a footnote at end of service' is the wordplay.
'footnote' becomes 'ps'.
'at end of' says to take the final letters.
The final letter of 'service' is 'e'.
'a'+'ps'+'e'='APSE'
'in' is the link.
(Other definitions for apse that I've seen before include "Large recess in church" , "Recess at eastern end of a church" , "Niche in church" , "Architectural feature in a church" , "Recess in church wall" .)