City in Europe being overlooked by church (5)
I believe the answer is:
essen
'city in europe' is the definition.
(Essen is a German city)
'being overlooked by church' is the wordplay.
'being' becomes 'essence' (essence can mean something's very being).
'overlooked by' is a deletion indicator.
'church' becomes 'CE' (abbreviation for Church of England).
'essence' with 'ce' removed is 'ESSEN'.
(Other definitions for essen that I've seen before include "Industrial city of northwest Germany" , "city in the Ruhr valley" , "German industrial city on the Ruhr" , "German place name" , "Krupp HQ (Ger.)" .)