Asia, including Cambodia, is a recognized hotspot for emerging infectious diseases (EIDs), particularly zoonotic and vector-borne infections. Recent emergences of coronaviruses (CoVs), such as sarbecoviruses (SARS-CoV-1 and the SARS-CoV-2), underscore the ongoing zoonotic transmission risk, but their prevalence and evolution in Rhinolophid bats remain poorly understood due to limited sampling. The discovery of SARS-CoV-2 related viruses in archived bat samples collected in Cambodia as early as 2010 reinforces the urgent need for enhanced surveillance and characterization of these viruses to better assess their emergence potential and public health risks. The re-emergence of chikungunya virus (CHIKV) in Cambodia in 2011 and 2020 highlights the virus evolution and the risk of re-emergence worldwide. It exemplifies the need for effective response strategies to EIDs. Insights from viral kinetics and immune response studies of CHIKV infections can improve treatment and prevention. Building on studies of bat CoVs and CHIKV, our work aims to enhance general prevention and control strategies for EIDs in Cambodia and beyond. A major aim of this work was to assess the diversity of CoVs in multiple bat species in Cambodia through longitudinal surveillance, and to characterize viruses of interest. Over three years, 1,462 bats were sampled and analyzed, revealing extensive and diverse CoVs co-circulation. Metatranscriptomic and amplicon sequencing generated 33 complete sarbecovirus genomes, revealing four novel lineages associated with different Rhinolophus species. Our study highlights the rapid migration and recombination of sarbecovirus lineages over short distances and timescales and identifies two novel viral groups with receptor-binding domains similar to those of SARS-CoV-2, capable of mediating entry into cells expressing human ACE2, suggesting potential zoonotic risk. In parallel, our study explored the viral kinetics, immune responses, and the potential of monoclonal a