Overweight, obesity, and poor health is becoming a global concern for defence force personnel. Conventional nutrition guidelines are being questioned for their efficacy in achieving optimal body composition and long-term health. This study compared the effects of a 12-week low-carbohydrate, high-fat diet with a conventional, high-carbohydrate, low-fat diet on weight reduction and metabolic health outcomes in at-risk New Zealand Defence Force personnel. In this randomised controlled trial, 41 overweight personnel were assigned to intervention and control groups. Weight, waist circumference, fasting lipids, and glycaemic control were assessed at baseline and at 12 weeks. Within-group change scores were analysed using the t statistic and interpreted using a p < 0.05 level of statistical significance. Between-group mean differences and confidence intervals were analysed using effect sizes and magnitude-based inferences. Twenty-six participants completed the trial (14 intervention, 12 control). Both groups showed statistically significant weight and waist circumference reductions; the intervention group significantly reduced triglycerides and serum glucose and significantly increased high-density lipoprotein cholesterol (HDLc). Relative to control, the intervention group showed small, possibly to likely beneficial effects for weight, triglycerides, glucose, insulin, and homeostasis model assessment of insulin resistance; moderate, likely beneficial effects for HDL cholesterol, triglyceride:HDLc ratio and HbA1c; and a small, likely harmful effect for low-density lipoprotein cholesterol. This dietary approach shows promise for short-term weight loss and improved metabolic health outcomes conditions compared with mainstream recommendations. It should be offered to defence force personnel at least as a viable alternative means to manage their weight and health.