The present research aimed to analyze the modification in performance, body composition, and autonomic modulation of reverse and traditional linear training periodization in amateur triathletes. We analyzed running and swimming performance, strength manifestation, body composition, and autonomic modulation before and after a traditional linear training periodization (four weeks of volume-based training plus four weeks of intensity-based training plus two-week tapering), a reverse linear training periodization (four weeks of intensity-based training plus four weeks of volume-based training plus two-week tapering), and a free training control physical active group (10-week free training) in 32 amateur athletes. Independently of the periodization model, the combination of two four-week mesocycles followed by a two-week taper is an efficiency strategy to avoid overreaching, obtaining an increase in parasympathetic modulation. Moreover, both types of training periodization proposed in this study do not modified body composition of amateur triathletes. Also, compared with traditional periodization, reverse periodization efficiently improves horizontal jump performance. Finally, reverse and traditional periodization were an effective strategy to improve running biomechanical, performance, and physiological variables, as well as efficient periodization strategies to improve swimming technical ability, aerobic, and anaerobic swimming performance.