Although the etymology of apothecary relates to a 'storehouse,' the current usage of the term is with reference to a person or his "office" (i.e., practice/ vocation) in pharmacy.
As such, its adjectival use with smell is bound to have hilarious outcomes.
However, should one insist on using such an expression, merely making an adjectival 'use' of the noun itself should be acceptable.
It had a clear apothecary smell.
Luckily, the word already sounds like an adjective, too.
apothecarial
adj. Characteristic of an apothecary
Walton:
Colard, a barber-surgeon, illustrated the apothecarial duties that a surgeon might perform when he wrote, I bequethe to John my sone all my instruments of ...
Roberts:
Inside, you'll sense a curious apothecarial smell, traced to the shelves lined with old pots and jars (labeled in Latin).
'Mama Earth' on Infobarrel:
Gin is derived predominantly from juniper berries, and mixed with herbs and spices to create its strange apothecarial smell.