Background: CrossFit® has become a popular and effective training methodology. This study aimed to compare the effects of a four-week CrossFit training program and analyze the inter-individual variability on body composition (fat mass and fat-free mass) and physical fitness (push-ups, military press, back squat, deadlift, countermovement jump (CMJ), sit-ups, and 30 m sprint speed) in novice and advanced practitioners. Methods: A quasi-experimental design was used, with single-blinded (evaluators) and 2 parallel groups: novices (n = 10; age = 22.30 ± 0.81) and advanced practitioners (n = 11; age = 22.80 ± 1.41). The intervention consisted of 3 weekly 75 min sessions (4 weeks), with pre- and post-assessments. A two-factor mixed ANOVA and inter-individual analyses to classify responders (Rs) and non-responders (NRs) were performed. Results: No significant interaction effects were found. However, the novice group significantly improved back squat performance (p = 0.031). Inter-individual analysis showed higher proportions of Rs in the novice group for back squat (40%), deadlift (20%), military press (10%), CMJ (10%), sit-ups (30%), push-ups (30%), and 30 m sprint speed (10%) compared to the advanced group. Conclusions: CrossFit program did not significantly affect body composition, but novices exhibited significant back squat improvements. Considering experience levels can enhance training outcomes.