Zoos play a vital role in managing and conserving a wide range of threatened species and in enhancing their populations in natural habitats through captive breeding and reintroduction programmes. Most small felids are poor breeders in zoos, owing to a range of issues such as spatial constraints, diet, disturbance from visitors, small population size, social grouping and other environmental factors in the exhibits. Many of these factors have also been found to influence the glucocorticoid levels among them. Chronic elevations in glucocorticoids can ultimately lead to psychological and physiological problems, eventually affecting reproduction and fitness. We assessed the influence of four biological and seven environmental factors on stress level linked to psychological (stereotype), and physiological (Faecal Glucocorticoid Metabolite, FGM) conditions and positive welfare behaviour (active and inactive) among 14 jungle cats Felis chaus managed at three zoos in Indian (two in Kerala and one in Maharashtra) during May 2014–March 2017. Stereotype, a behavioural indicator of stress, and welfare behaviour were assessed through 336 h daylight focal sampling and physiological stress following non-invasive FGM extraction using Enzyme-Immunoassay (EIA) from 63 fresh faecal samples. Overall, jungle cats spent more time on inactive (72%) compared to active behaviour (23%) and 5% on stereotypic behaviour. On average, the jungle cats had 43.3 ng/g of FGM. The Principal Component Analysis on 11 independent factors revealed that daylight hour did not influence active, inactive and stereotype behaviours. In addition, age also had no significant influence on FGM levels. Binary logistic regression revealed that active behaviour was more likely to be observed in cats fed live chicken, housed on natural substrate and in females. Inactive behaviour was significantly lower in younger cats, but higher in cats managed with hideouts. Our results suggest that cats housed with non-relatives and in enclosures lacking hideouts have higher rates of stereotype. Multiple regression analyses on behaviour indicate that active behaviour was significantly higher in cats when the arrival age at the zoo was <1 year, among females compared to males, fed live chicken compared to beef, when managed in natural compared to artificial enclosures and in enclosures without hideouts. Remarkably, inactive behaviour increased significantly with increase in visitor intensity and when cats fed beef compared to live chicken. The stereotypic behaviour was significantly lower in females and higher when the arrival age at the zoo was >1 year. It was also the case when the cats were fed beef vs. whole live chicken, when managed in enclosures without hideouts, and also when managed with unrelated conspecifics compared to those kept in enclosures with hideouts and in solitary condition. The FGM levels were significantly higher among males but lower among cats managed in natural and larger enclosures, and enclosures with hideouts, when compared to those managed in artificial, smaller enclosures and enclosures without hideouts. We recommend the provision of larger (>29 m2) natural enclosures with hideout facilities, management in solitary condition or in social groupings with related conspecifics and feeding of live prey to promote positive welfare and reduce psychological and physiological stress among the jungle cats in zoos.