Introduction: Kenya Malaria Strategy(KMS) 2019–2023 targets to reduce malaria incidences and deaths by at least 75% by 2023. In 2020, there was a decline in facilities reporting inpatient malaria data by 18%, reducing the number of malaria admissions in the country. Therefore, we aimed to assess inpatient Malaria cases, case management and Data Quality Audits in low and high malaria endemic counties of Kenya. Methods: We used a mixed-method approach in Makueni, Taita-Taveta and Lamu counties. We retrieved reports from Kenya Health Information System(KHIS), reviewed inpatient registers and medical records for malaria data from admitting facilities. All malaria records for clients attended, 2020-2022 were eligible. We administered questionnaires to healthcare workers in the visited facilities to assess malaria case management. Descriptive statistics were performed. Results: Of the 23 inpatient facilities visited, only 52% reported into the KHIS platform; Makueni at 45%(5/11) and Lamu at 36%(4/11) contributed the highest number of facilities not reporting. A total of 131 malaria records were abstracted, ages ranging from three months to 72 years(median 22 years), with a Case fatality rate of 2.3%. Makueni county being a low-risk county, had more cases than Lamu county at 33%(44/131). On diagnosis, 46%(60/131) were uncomplicated, while 1.53% were clinical malaria admissions. Those treated with Artemether-lumefantrine(AL) and Artesunate drugs were 61%(80/131) and had the shortest hospital stay, 1–7 days. Only 51%(36/70) of healthcare workers were trained in malaria case management, and 44%(16/36) were clinicians. On International Classification of Diseases 10/11, 59%(13/22) of Health records officers were trained, and 36%(10/28) of laboratory officers were not conducting malaria species quantification.   Conclusions: Patients treated with both Artemether-lumefantrine and Artesunate drugs were below the 80% KMS target and had shorter hospital stay. There were gaps in malaria diagnosis and management of cases.