Nick puts holy books in new church (5)
I believe the answer is:
notch
'nick' is the definition.
(both can mean a small cut or impression)
'holy books in new church' is the wordplay.
'holy books' becomes 'OT' (Old Testament).
'in' is an insertion indicator.
'new' becomes 'n' (common abbreviation eg NT for New Testament).
'church' becomes 'ch' (abbreviation on maps etc).
'n'+'ch'='nch'
'ot' inserted within 'nch' is 'NOTCH'.
'puts' acts as a link.
(Other definitions for notch that I've seen before include "Nick; small cut" , "small score?" , "Indentation - step up" , "Point or degree in a scale" , "Salad plant, garnish" .)