Background Healthcare-associated infections (HAIs) are a leading adverse event in healthcare delivery. Despite Kenya's robust National Infection Prevention and Control (IPC) Policy and Strategic Plan, a profound policy-to-practice gap persists at the institutional level. This study explored context-specific structural, behavioral, and administrative barriers hindering IPC implementation at a public referral hospital to inform localized policy tailoring. Methods We conducted a cross-sectional qualitative study at a level V teaching and referral hospital in Kenya. Seven key informant interviews were held with five IPC committee members/providers and two departmental managers. Data from audio recordings and field notes were transcribed, translated, and analyzed via thematic content analysis using QSR NVivo V.12. Results Seven major themes emerged: (1) IPC Training and Knowledge Retention, (2) Workforce Strain and Triaging of IPC, (3) Resource Scarcity and a Disabling Environment, (4) The Community-Hospital Interface, (5) Governance and Policy-to-Practice Lag, (6) IPC Surveillance and Monitoring, and (7) Behavioral Drivers (Attitude, Ignorance, Accountability). Financial and human resource constraints directly undermine continuous medical education, workforce ratios, WASH infrastructure functionality, and the local adaptation of national guidelines. Conclusion A substantial policy-to-practice gap persists at the facility level due to severe structural, resource, and behavioral constraints. To bridge this gap, hospital leadership must transition from reactive crisis management to proactive, continuous medical education and sustainable WASH infrastructure development. Effective IPC implementation requires national frameworks to be dynamically adapted and tailored to the operational realities and resource limitations faced by frontline healthcare workers.