The Philippines is the largest Christian-majority country in Asia. With church gatherings playing a vital role in the nature of Christianity in the Filipino culture, the advent of the coronavirus disease (COVID-19) pandemic in the Philippines posed challenges to public religious practices amid efforts to mitigate COVID-19 community transmission. Various policy pronouncements from both the government-led Inter-Agency Task Force (IATF) on Emerging Diseases and the church-led Catholic Bishops’ Conference of the Philippines (CBCP) were issued. These guidelines were implemented in order to address the two-pronged problem on healthcare and religious obligations. While these guidelines were initially contributory to the mitigation of disease transmission, varied compliance by Filipinos was observed through the progression of the pandemic. Considering the value that church gatherings and religion play in the lives of the Filipino people, further studies on COVID-19 transmission in the church should be conducted in order to develop more efficient policies and guidelines on the practice of religion, particularly for religious gatherings. Furthermore, a more synergistic state and church cooperation must be encouraged in order to arrive at solutions that will mutually address the concomitant problems of the COVID-19 pandemic.