Spirit from church beneath German city (7)
I believe the answer is:
essence
'spirit' is the definition.
(essence can mean something's spirit or heart)
'church beneath german city' is the wordplay.
'church' becomes 'CE' (Church of England).
'beneath' says to put letters next to each other (in a down clue, some letters go below others).
'german city' becomes 'essen' (city in Germany).
'ce' after 'essen' is 'ESSENCE'.
'from' is the link.
(Other definitions for essence that I've seen before include "Indispensable" , "Scent; core" , "Nature - concentrate" , "Attar" , "Cologne, perhaps?" .)