Background Food insecurity is associated with poor nutritional health outcomes. Prescribing fresh fruits and vegetables in healthcare settings may be an opportunity to link patients with community supports to promote healthy diets and improve food security. This mixed methods study evaluated the impacts of a fresh food prescription pilot program. Methods The study took place at two Community Health Centre locations in Guelph, Ontario, Canada. Sixty food insecure patients with ≥1 cardio-metabolic condition or micronutrient deficiency participated in the intervention. Participants were prescribed 12 weekly vouchers to Community Food Markets. We conducted a one-group pre-post mixed-methods evaluation to assess changes in fruit and vegetable intake, self-reported health, food security, and perceived food environments. Surveys were conducted at baseline and follow-up and semi-structured interviews with participants were conducted following the intervention. Results Food security and fruit and vegetable consumption improved following the intervention. Food security scores increased by 1.6 points, on average (p < 0.001). Consumption of fruits and ‘other’ vegetables (cucumber, celery, cabbage, cauliflower, squashes, and vegetable juice) increased from baseline to follow-up (p < 0.05). No changes in self-reported physical or mental health were observed. Qualitative data suggested that the intervention benefited the availability, accessibility, affordability, acceptability, and accommodation of healthy foods for participating households. Conclusions Fresh food prescription programs may be a useful model for healthcare providers to improve patients’ food environments, healthy food consumption, and food security.