Insufficient physical activity (PA) is associated with low cardiorespiratory fitness, which favors cardiovascular and other noncommunicable diseases. Additionally, it evidentially affects mental health. Considering the WHO PA guidelines, CrossFit® represents a versatile exercise program that combines aerobic and resistance training with mobility and could help reduce disease incidences among sedentary people. Yet, long-term CrossFit research is sparse. We conducted a nine-month intervention (≥ 2 CrossFit workouts/week) in 16 beginners (14 males, 35 ± 6.8 years, 180 ± 8.6 cm, 85. 5 ± 19.1 kg). As a primary endpoint, VO2max was assessed at baseline, four, and nine months. A repeated-measures ANOVA and Pearson correlation were conducted. Well-being was investigated by the WHO-5 Index pre- and post-intervention. For exploratory purposes, body composition and heart rate recovery (HRR) were tracked. In a second step, all males were categorized into two groups based on body fat percentage and analyzed by repeated measures ANOVA again. The main outcome was an 11.5% VO2max improvement with a large effect (p < 0.01, η p2 = 0.27). Strong negative correlations between baseline VO2max and its progression after nine months (p = 0.006, r = − 0.654) were found. Well-being increased by 8.7% (p = 0.024, d = 0.51). HRR improved both at 1 min (p < 0.05, η p2 = 0.34) and at 5 min (p < 0.05, η p2 = 0.27) post-exercise. Resting metabolic rate increased by 2.2% (p = 0.042). Analysis by group revealed improved HRR at 1 min (p < 0.05, η p2 = 0.62) only for the “ high body fat” group. This study reveals the potential of CrossFit to enhance physiological and psychological health in beginners. For more robust results, larger sample sizes with a higher proportion of women are needed.