The purpose of this study was two-fold: (a) to describe and analyse the relationship of the in-season variations of external and internal intensity metrics as well as well-being measures across different periods of a semi-professional soccer season (early-, mid- and end-season); and (b) to describe training monotony (TM) and training strain (TS) for 20 weeks in a semi-professional soccer season. Eighteen semi-professional players (age: 29 ± 4.1) from the Asian First League team participated in this study. The players were monitored for 20 consecutive weeks during in-season for external training intensity, internal training intensity and well-being parameters. The in-season was organized into three periods: early-season (weeks 1–7); mid-season (weeks 8–13); and end-season (weeks 14–20). Total distance (TD), high-speed running distance (HSRD), sprint distance, rate of perceived exertion (RPE), session-RPE (s-RPE), TM, TS, heart rate average and maximum, as well as sleep quality, stress and muscle soreness were collected. Results revealed that TD, HSRD and sprint distance (total values) were meaningfully greater during end-season than in the early-season. RPE showed a significantly highest value during the end-season (4.27 AU) than in early- (3.68 AU) and mid-season (3.65 AU), p < 0.01. TS showed significant differences between early-season with mid-season (p = 0.011) and end-season (p < 0.01), and the highest value occurred in week 17 during end-season (6656.51 AU), while the lowest value occurred in week 4 during early-season (797.17 AU). The average TD periods showed a moderate to large correlation with RPE, sleep and s-RPE at early-, mid- and end-season. Increasing the training intensity without considering the well-being of the players affects the performance of the team. Examining processes of the relationship between training intensity and other psychological indicators among players will probably be effective in training planning. Sports coaches and fitness professionals should be wary of changes in TM and TS that affect players performance. Therefore, to better control the training, more consideration should be given by the coaches.