The COVID-19 pandemic required an efficient uplift of health professional competencies. Accordingly, the Sri Lankan Ministry of Health implemented novel online training for 50 hospitals in COVID-19 management. This study aimed to evaluate the impact of these online training programs to enable refinements for future implementation. Cluster sampling selected seven hospitals for the descriptive cross-sectional study. An interviewer-administered questionnaire was provided to 840 randomly selected health staff who participated in the training programs, and 637 responded. The most useful, satisfied, and effective training was ‘Use of Personal Protective Equipment’. The highest-ranked advantages of online training were time and cost savings, while more interaction and effectiveness were for face-to-face training. Most participants (>75%) preferred online training during the pandemic, but approximately 33% preferred face-to-face training under normal conditions. Hospital, age, gender, staff, educational, and healthcare experience categories were significantly associated with the perceived effectiveness and preference for online training versus face-to-face training in different circumstances. While these novel online training programs were considered effective and preferred during the pandemic, future utilization for professional development programs in non-pandemic environments needs to account for health professional preferences varying with contextual factors, integration with strategies for interaction, and provision of required resources.