Background: The impact of COVID-19 in Africa remains poorly described. We examined hospitalisation trends for all medical causes, clinician-diagnosed pneumonia admissions, and inpatient mortality in Kenya two years before and across the first six waves of the pandemic. Methods: We conducted a hospital-based observational study of patients admitted to 13 public referral facilities in Kenya from January 2018 to December 2022. The pre-COVID-19 population included admissions before 1st March 2020. Time series models, adjusted for seasonality and hospital, compared observed and predicted trends. To estimate the impact of the COVID-19 pandemic, we calculated incidence rate ratios (IRR) from negative binomial mixed-effects models. Results: 357,631 patients were admitted across the 13 sites (range 15,354 to 67,241 per hospital). 45,349 patients (42.1%) were admitted to the adult medical wards. On the paediatric ward, 163,608 individuals (47.4%) were aged under five years and 36,227 individuals (10.5%) were aged five years and older. In comparison to the pre-pandemic period, hospitalisations reduced for adults (IRR 0.75, 95% CI 0.69–0.82) and paediatric cases (IRR 0.69, 95% CI 0.64–0.75). In-hospital deaths also declined for adults (IRR 0.83, 95% CI 0.77–0.89) and children (IRR 0.85, 95% CI 0.77–0.94). Adult pneumonia admissions increased (IRR 1.59, 95% CI 1.36–1.85), while paediatric cases decreased overall, (IRR 0.78, 95% CI 0.51–1.20), but became elevated in late 2021 compared to the pre-pandemic period. Conclusions: The COVID-19 pandemic did not cause a surge in hospitalisations in Kenya. However, pneumonia admissions among adults (but not children) increased significantly, with peaks aligning with the pandemic waves. These findings underscore the importance of syndromic inpatient surveillance in detecting and monitoring outbreaks.