Abstract Background Non‐human animals are natural hosts for the virus causing COVID‐19 (severe acute respiratory syndrome coronavirus 2 [SARS‐CoV‐2]) and a diversity of species appear susceptible to infection. Cats are of particular concern because of their close affiliation with humans and susceptibility to infection. Cats also harbour feline enteric coronavirus (FECV). Our objectives were to document the prevalence of SARS‐CoV‐2 and FECV in feline populations with high turnover and movement among households in the Central Valley of California, USA. Methods A cross‐sectional study of 128 shelter and foster cats and kittens in the Central Valley of California was performed from July to December 2020. PCR was performed on rectal and oropharyngeal samples to detect SARS‐CoV‐2 RNA and on rectal samples to detect FECV RNA. Results Among 163 rectal and oropharyngeal fluid samples gathered from sheltered and fostered cats and kittens in central California, SARS‐CoV‐2 nucleic acids were not detected from any cat or kitten. In contrast, FECV nucleic acids were detected in 18% of shelter‐housed cats; 83% of these positive samples were collected from cats housed in adjacent cages. Conclusions These data may be helpful when considering the allocation of resources to minimise the harm of FECV and SARS‐CoV‐2 in household pets and shelter environments.