Box in small house by church (5)
I believe the answer is:
hutch
'box' is the definition.
(thesaurus)
'small house by church' is the wordplay.
'small house' becomes 'hut' (I've seen this before).
'by' is a charade indicator (letters next to each other).
'church' becomes 'ch' (common abbreviation).
'hut'+'ch'='HUTCH'
'in' is the link.
(Other definitions for hutch that I've seen before include "Animal house" , "Cage for rabbit?" , "where rabbit lives?" , "Bunny box" , "Pen for small anivals" .)