ABSTRACT Surveillance of bat coronaviruses (CoVs) is of public health importance, as accumulating evidence suggests that bats are hosts of the three significant pandemic viruses, namely Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and SARS-CoV-2. Studies focused on identifying different bat CoVs species provides essential insights for preventing and controlling emerging zoonotic diseases. This systematic review evaluated molecular studies on bat CoVs, retrieving 890 articles from PubMed and Google Scholar. After applying selection criteria, 127 articles were included for full-text analysis. Among 54 countries studied, China accounted for the highest number of studies (26%, n = 33). The sample categories consisted of faecal, urine, guano, blood, tissues, oral, and rectal swabs. The molecular detection approaches included polymerase chain reaction (PCR) using species-specific, genus-specific, or broad-range primers. PCR assays targeting the partial RdRp gene (123–440 bp) were used in 94.5% (n = 120) of studies, followed by sequencing with Sanger or next-generation technologies. Full genome sequencing was only performed in approximately 33.9% (n = 43), with metagenomics approaches being used in 15.7% (n = 20) of the studies. The higher positivity rate of bat CoVs were detected in Asia. Globally, the most predominant bat species which tested positive for CoVs were Rhinolophus, Myotis, Miniopterus, Scotophilus, Eidolon, Chaerephon, Hipposideros, and Desmodus. Continuous bat coronavirus surveillance using molecular methods and full genome sequencing is of utmost importance in detecting and characterizing viruses at molecular level and establishing the genetic diversity of new and circulating viruses.