International research on prisoners demonstrates poor health outcomes, including chronic disease, with the overall burden to the community high. Prisoners are predominantly male and young. In Australia, the average incarceration length is 3 years, sufficient to impact long term health, including nutrition. Food in prisons is highly controlled, yet gaps exist in policy. In most Western countries prisons promote healthy foods, often incongruent with prisoner expectations or wants. Few studies have been conducted on dietary intakes during incarceration in relation to food policy. In this study detailed diet histories were collected on 120/945 men (mean age = 32 years), in a high-secure prison. Intakes were verified via individual purchase records, mealtime observations, and audits of food preparation, purchasing and holdings. Physical measurements (including fasting bloods) were taken and medical records reviewed. Results showed the standard food provided consistent with current dietary guidelines, however limited in menu choice. Diet histories revealed self-funded foods contributing 1–63% of energy (mean = 30%), 0–83% sugar (mean = 38%), 1–77% saturated fats (mean = 31%) and 1–59% sodium (mean = 23%). High levels of modification to food provided was found using minimal cooking amenities and inclusion of self-funded foods and/or foods retained from previous meals. Medical records and physical measurements confirmed markers of chronic disease. This study highlights the need to establish clear guidelines on all food available in prisons if chronic disease risk reduction is a goal. This study has also supported evidenced based food and nutrition policy including menu choice, food quality, quantity and safety as well as type and access to self-funded foods.