Background Environmental health services (EHS) in healthcare facilities (HCFs) are critical for providing a safe, functional healthcare environment, but little is known about their costs. Poor understanding of costs impedes progress towards universal access of EHS in HCFs. We developed frameworks of essential expenses that provide EHS and conducted an ex-post financial analysis of EHS in a network of medical research and training facilities in Lilongwe, Malawi serving an estimated 42,000 patients annually. Methods We estimated the cost of providing the following EHS: water, sanitation, hygiene, personal protective equipment use at the point of care, waste management, cleaning, laundry, and vector control. We developed frameworks of essential outputs and inputs for each EHS through review of international guidelines and standards, which we used to identify required expenses for EHS delivery and evaluate the completeness of costs data in our case study. For costing, we use a mixed-methods approach, applying qualitative interviews to understand facility context and review of electronic records to determine costs. We calculated initial costs to establish services and annual operations and maintenance.Results Available records contained little information on the upfront, capital costs associated with establishing EHS. Annual operations and maintenance totaled USD 220,427 for all EHS, although costs of essential inputs were missing from records. Annual operations and maintenance costs were highest for cleaning (USD 69,372) and waste management (USD 46,752).Discussion Missing expenses suggests that documented costs are substantial underestimates. Costs to establish services were missing predominantly because purchases pre-dated electronic records systems. Annual operations and maintenance costs are incomplete primarily because administrative records did not record sufficient detail to disaggregate and attribute expenses. Conclusions Electronic health information systems have potential to support efficient data collection. However, we found that existing records systems were decentralized and poorly suited to identify EHS costs. Our research suggests a need to better code and disaggregate EHS expenses to properly leverage records for costing. Frameworks developed in this study are a potential tool to develop more accurate estimates of the cost of providing EHS in HCFs.