Bats face diverse challenges that cause global bat population declines, including habitat loss and roost disturbance. Additionally, negative perceptions of bats and their potential role in several zoonotic diseases have led to actions against bats. We documented existing knowledge and perception of bats through interviews with 151 participants of fifteen tribes in Northern Uganda in 2020 and conducted a sensitization campaign that prevented planned actions against bats. The interviews revealed distinct firm beliefs, negative perceptions, limited knowledge on bats, and the influence of media in shaping actions against bats. In addition, modified landscapes and habitat loss increased encounters and subsequent deterioration of relations between humans and bats. Targeted threats towards bats were exacerbated by public misinformation during the SARS-CoV-2 pandemic. No deliberate conservation efforts exist, and negative perception largely hampers the implementation of bat conservation in Northern Uganda. Importantly, the study also demonstrates that sensitization campaigns can be effective tools to protect bats in the short term. Regular sensitizations and education are recommended for sustainable changes in attitudes to and coexistence with bats.