Coup in place beginning to shake church (6)
I believe the answer is:
putsch
'coup' is the definition.
('putsch' can be a synonym of 'coup')
'place beginning to shake church' is the wordplay.
'place' becomes 'put' ('put' can be a synonym of 'place').
'beginning to' indicates taking the first letters.
'church' becomes 'ch' (common abbreviation).
The initial letter of 'shake' is 's'.
'put'+'s'+'ch'='PUTSCH'
'in' is the link.
(Other definitions for putsch that I've seen before include "Sudden illegal acquisition of power" , "Change of government by force" , "Revolutionary uprising" , "Violent attempt to seize power" , "A sudden political uprising" .)