Systemic use: Atropine is metabolised in the liver by oxidation and conjugation to give inactive metabolites. About 50% of the dose is excreted within 4 hours and 90% in 24 hours in the urine, about 30 to 50% as unchanged drug.
Atropine Injection BP Minijet UK Summary of Product Characteristics, International Medication Systems (UK) Ltd, updated October 2005

Ocular use: Atropine is also absorbed by mucous membranes but less readily from the eye and skin, although significant toxicity can sometimes occur through absorption of excessive eye drops. Atropine is metabolised by hepatic oxidation and conjugation to inactive metabolites, with about 2% undergoing hydrolysis to tropine and tropic acid. About 30% of the dose is excreted unchanged in the urine. Only trace amounts of the dose are eliminated in the faeces.
Minims Atropine Sulphate 1%, Eye drops solution UK Summary of Product Characteristics, Bausch & Lomb U.K Limited, updated July 2012