Shell of ruined monastery, deserted by man (6)
I believe the answer is:
oyster
'shell' is the definition.
(oyster shell is a kind of shell)
I don't understand how the remainder of the clue works.
Can you help me to learn more?
(Other definitions for oyster that I've seen before include "Parent of the pearl" , "Maybe grey" , "Pearl-yielding shellfish" , "Bivalve that may nurture a pearl" , "Pearl's home?" .)