The aim of the study was to investigate the habitat, characteristics, and the health status of cat colonies under supervision of a trap-neuter-return program, the distance of the cats maintained with respect to their caregivers as a measure of the animals’ fear of or confidence in humans, and relationships between these factors with regard to animal welfare. Thirteen managed cat colonies in different urban habitats were visited twice (1st and 2nd visit) by a team of two observers. The assessment of health and other welfare parameters was based on direct observation at the feeding sites, caregiver inquiry, and photo analysis. Potential associations between the parameters were analyzed at an individual level (e.g., injuries related to sex and neuter status) or at group level (e.g., percentage of animals with impaired health). Interobserver reliability was high for all indicators. Most cats were in a good state of health, and most were already neutered. The lower the percentage of clean feeding places, the higher was the percentage of thin animals (1st/2nd visit: rs = −0.72/−0.58, P = 0.01/0.04) and the percentage of cats showing apathetic behavior (1st/2nd visit: rs = −0.54/−0.58, P = 0.06/0.04). The larger the group size, the higher was the percentage of cats with hair coat deviations (1st/2nd visit: rs = −0.73/−0.79, P = 0.01/<0.01). There were also some associations between sex/neuter status and health. Intact males were most likely to be injured, whereas no injuries were observed in females. The results suggest that feeding site characteristics, such as group size and cleanliness of feeding places, as well as sex and neuter status can have an impact on the health status and thus welfare of colony cats. If caregivers offered diluted milk or treats, a higher percentage of cats approached to close proximity (1st/2nd visit: diluted milk: P = 0.02/0.01; treats: P = 0.04/0.04). The offering of treats likely strengthened the animal-human relationship. Indicators such as the percentage of very thin animals, cats showing altered, apathetic behavior, cats with hair coat deviations, injuries, as well as the percentage of animals approaching within close proximity to their caregiver seem to be useful indicators for the welfare surveillance of cats in managed colonies in terms of validity, because we found associations with environmental factors, the care provided to the cats, or cat colony characteristics.