A critical challenge in today's dynamic and turbulent organizations is to retain capable, competent, and skilled workforce. This reality has an enormous impact on healthcare institutions which undergo a catalogue of challenges in health service delivery. The ultimate objective of this study was to assess challenges facing the performance of Catholic healthcare facilities in Tanzania in three dimensions; human resources, leadership and managing of financial resources. A mixed method approach and case study research design were undertaken to assess the challenges facing the performance of Catholic healthcare facilities in Tanzania. Turiani and Mikumi Hospitals in Morogoro Region were taken as the empirical study areas of the research. A total of 121 participants out of 123 (98%) were involved in the study. Self-administered structured questionnaires, interview, observation and document analysis were used as tools for collecting quantitative and qualitative data. Descriptive and inferential statistics were employed through the use of IBM SPSS Statistics v.20. The research instruments had an excellent internal consistency with Cronbach's alpha of 0.962. The factor analysis was suitable and appropriate with KMO test of 0.865 and Bartlett's test for Sphericity of (P < 0.001). The findings reveal that, Catholic healthcare is experiencing challenges arising from deficiency in managing human resource. These challenges include weak leadership; inadequacy in managing financial resource, divided loyalty, lack of engagement, and a decline in both commitment and enthusiasm for work. These challenges have stalled health care delivery and have gradually weakened performance in health services delivery. In order to improve this, the leadership, management team and governing board of the hospitals should work closely with employees of Turiani and Mikumi hospitals to realign themselves with the hospitals' vision, mission and goals to rescue the future of Catholic healthcare. The Tanzania Catholic Church Health Policy of June, 2008 is hereby highly recommended as a yardstick for continuous improvement.