It’s burned in church — not so effectively at first (7)
I believe the answer is:
incense
'it's burned' is the definition.
(incense is burned for its smell)
'in church not so effectively at first' is the wordplay.
'church' becomes 'CE' (abbreviation for Church of England).
'at first' indicates taking the first letters.
The first letters of 'not so effectively' is 'nse'.
'in'+'ce'+'nse'='INCENSE'
(Other definitions for incense that I've seen before include "make you very cross" , "It produces a fragrant smell when burned" , "Nettle" , "Sweet-smelling spice" , "Make one see red" .)