Preside over church with atmosphere (5)
I believe the answer is:
chair
'preside over' is the definition.
'church with atmosphere' is the wordplay.
'church' becomes 'ch' (common abbreviation).
'with' says to put letters next to each other.
'atmosphere' becomes 'air' ('air' can be a synonym of 'atmosphere').
'ch'+'air'='CHAIR'
(Other definitions for chair that I've seen before include "Lead" , "Seat (of learning?)" , "conduct" , "Senior academic post" , "president" .)