Abstract Background Infectious bronchitis virus (IBV) is classified as a highly contagious viral agent that causes acute respiratory, reproductive and renal system pathology in affected poultry farms. Molecular and serological investigations are crucial for the accurate diagnosis and management of IBV. Objectives The purpose of this study was to determine the seroprevalence of IBV and to characterise the circulating IBV in poultry farms in Sabah Province, Malaysia. Methods To determine IBV antibodies, a total of 138 blood samples and 50 organ samples were collected from 10 commercial broiler flocks in 3 different farms by using the enzyme‐linked immunosorbent assay (ELISA) (IDEXX Kit) and reverse transcription‐polymerase chain reaction (RT‐PCR) followed by sequencing. Results A total of 94.2% (130/138) of the samples were seropositive for IBV in the vaccinated flock, and 38% (52/138) of the birds was the IBV titre for infection. The selected seropositive samples for IBV were confirmed by RT‐PCR, with 22% (11/50) being IBV positive amplified and sequenced by targeted highly conserved partial nucleocapsid (N) genes. Subsequently, phylogenetic analysis constructed using amplified sequences again exposed the presence of Connecticut, Massachusetts, and Chinese QX variants circulating in poultry farms in Sabah, Malaysia. Conclusions The unexpectedly increasing mean titres in serology indicated that post infection of IBV and highly prevalent IBV in selected farms in this study. The sequencing and phylogenetic analysis revealed the presence of multiple IBV variants circulating in Malaysian chicken farms in Sabah, which further monitoring of genetic variation are needed to better understand the genetic diversity.