BACKGROUND: High compliance to infection prevention and control (IPC) is vital to prevent health care-associated infections. In the worst 2014-2015 Ebola-affected district in Sierra Leone (Kenema), we assessed (a) average yearly IPC compliance (2016-2018) using a National IPC assessment tool in the district hospital and peripheral health units (PHUs), and (b) gaps in IPC activities, infrastructure and consumables in 2018. METHODS: This was a cross-sectional study using secondary program data. RESULTS: At the district hospital, compliance increased from 69% in 2016 to 73% in 2018 (expected minimal threshold = 70%; desired threshold ≥ 85%). Compliance for screening/isolation facilities and decontamination of medical equipment reached 100% in 2018. The two thematic areas with the lowest compliance were sanitation (44%) and sharps safety (56%). In PHUs (2018), the minimal 70% compliance threshold was not achieved in two (of 10 thematic areas) for Community Health Centers, four for Community Health Posts, and five for Maternal and Child Health Units. The lowest compliance was for screening and isolation facilities (range: 33-53%). CONCLUSION: This baseline assessment is an eye opener of what is working and what is not, and can be used to galvanize political, financial, and material resources to bridge the existing gaps.