This qualitative research aimed to identify the challenges faced by local government units (LGUs) in Bohol during the COVID-19 pandemic, the measures implemented in response, and the gaps and opportunities for improvement in their pandemic response efforts. Focused Group Discussions were conducted with sector representatives from first-, second-, and third-income class LGUs in Bohol, and qualitative data were analyzed thematically using the Qualitative Data Analysis Miner tool. The study revealed that the LGUs faced various challenges during the pandemic, including a lack of resources, unpreparedness, communication gaps, and logistical issues. However, the LGUs were able to implement best practices such as sound action through the provision of assistance, actions reflecting a sense of urgency, flexibility, collaboration, and fairness, preparedness, and benchmarking. As such, the study recommends that the LGUs focus on improving their preparedness and resources, optimizing communication and logistics management, exploring more innovative approaches, building collaborations and partnerships, and tailoring education efforts to specific populations. By continuously evaluating and improving their pandemic response efforts, the LGUs can better protect and serve their communities.