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Non-communicable diseases (NCD) are associated with high costs for healthcare systems. We evaluated changes in total costs, comprising direct and indirect costs, due to a 24-month non-randomized, controlled lifestyle intervention trial with six measurement time points aiming to improve the risk profile for NCDs. Overall, 187 individuals from the general population aged ≥18 years were assigned to either the intervention group (IG; n = 112), receiving a 10-week intensive lifestyle intervention focusing on a healthy, plant-based diet; physical activity; stress management; and community support, followed by a 22-month follow-up phase including monthly seminars, or a control group (CG; n = 75) without intervention. The complete data sets of 118 participants (IG: n = 79; CG: n = 39) were analyzed. At baseline, total costs per person amounted to 67.80 ± 69.17 EUR in the IG and 48.73 ± 54.41 EUR in the CG per week. The reduction in total costs was significantly greater in the IG compared to the CG after 10 weeks (p = 0.012) and 6 months (p = 0.004), whereas direct costs differed significantly after 10 weeks (p = 0.017), 6 months (p = 0.041) and 12 months (p = 0.012) between the groups. The HLCP-2 was able to reduce health-related economic costs, primarily due to the reduction in direct costs.