The nutritional and health perceptions of inmates are crucial to their overall well-being. However, limited research has been conducted on this topic. This study aimed to assess the nutritional and health perception state of male inmates in eleven prisons in Israel. A cross-sectional study was conducted between February and September 2019 with 176 voluntary participants. Structured questionnaires were used to collect data on socio-demographic characteristics, healthy habits, subjective health status, and prison situation variables. The study found that the prevalence of overweight (40%) and obesity (18.1%) among 18–34-year-old inmates was significantly higher than in the reference Israeli population. Short detention periods (up to one year) predicted less weight gain, while older age predicted poorer health status. Better emotional status significantly predicted better subjective health status among male inmates. There is a need for nutrition interventions to improve the health of inmates. The significant weight gain during incarceration and the associated lower health index and stress highlights the importance of increasing knowledge and promoting a healthier lifestyle in incarceration as early as possible and continuing over time.