Tom, say, fencing off grand and small grain store (9)

'grain store' is the definition.
(building that stores malt)

'tom say fencing off grand and small' is the wordplay.
'tom say' becomes 'male' (tom can mean a male cat).
'fencing off' indicates putting letters inside.
'grand' becomes 'thou' (synonyms).
'and' says to put letters next to each other.
'small' becomes 's' (abbreviation - e.g. clothes size).
'thou'+'s'='thous'
'male' placed around 'thous' is 'MALTHOUSE'.