Seat in church beneath mountain (5)
I believe the answer is:
bench
'seat' is the definition.
(I know that seat can be written as bench)
'church beneath mountain' is the wordplay.
'church' becomes 'ch' (common abbreviation).
'beneath' is a charade indicator (letters next to each other) (in a down clue).
'mountain' becomes 'ben' (ben is a kind of mountain).
'ch' after 'ben' is 'BENCH'.
'in' is the link.
(Other definitions for bench that I've seen before include "Magistrates collectively" , "Group of magistrates" , "Exhibit at dog show" , "Pew or settle" , "Long seat or worktable" .)