A high level of physical fitness is one important factor for optimal performance in Special Operation Forces (SOF). Still, information about physical training for SOF operators is not easily accessible. This study aimed to implement and assess a new training concept in the Norwegian Navy SOF. A longitudinal study where 22 operators completed a 6-month linear periodization (LP), followed by a 6-month nonlinear periodization (NLP) program. Both protocols were block periodized, focusing on either strength or aerobic capacity. A battery of tests covering strength, endurance, power, mobility, and body composition was performed, and individual capacity analyses were established. A training week consisted of 5 to 6 sessions including 1 or 2 individualized sessions directed towards improving the weakest capacity. The LP had a clear effect on mobility (19 ± 9%), abdominal strength (25 ± 16%), upper body power (PowerUB; 6 ± 9%), standing long-jump (3 ± 6%), pull-ups (24 ± 31%), agility (2 ± 4%), V[Combining Dot Above]O2max (2 ± 3%), fat percent (-5 ± 31%), and muscle mass (1 ± 3%). The NLP increased abdominal strength (15 ± 17%), standing long-jump (3 ± 4%), and anaerobic capacity (10 ± 8%), whereas V[Combining Dot Above]O2 max (-3 ± 4%) and PowerUB (-2 ± 7%) decreased. Additional analyses showed clear increases among those individually instructed to improve strength. Results support the benefits of combined periodized programming and individualized training sessions among SOF operators with initially good fitness levels. Largest effects were observed in the first phase with the LP. However, subsequent NLP additionally increased anaerobic and jumping capacity, possibly due to more frequent muscular endurance and power training. Because of frequent interruptions, the LP tended to be more difficult to follow than the NLP and is suggested when continuity is possible, whereas an NLP is recommended for maintenance and when standing on national preparedness.