This study aimed to explore the association between various levels of training-energy expenditure (TrEE) and nutritional response during the phases of periodization among male collegiate rugby players. Seventeen Japanese male collegiate rugby players were enrolled in the study. Their TrEE and dietary intake were assessed each day during three separate microcycle training phases in the preparatory phase of periodization (P1 and P2: general training phase consisting of two sessions per day over the term during which the school held classes and during a summer vacation, respectively; and P3: intensive training phase consisting of four sessions per day during a summer vacation) using the factorial method and dietary records, respectively. The TrEE for P3 (1644±273 kcal) was significantly higher than that for P1 (891±230 kcal). However, the total energy intake (EI) for P3 (3274±889 kcal) was significantly lower than that for P1 (3978±938 kcal). The daytime (after waking in the morning and before the evening training session) EI (242±159 kcal) and protein intake (19±12 g) from the ‘high-protein foods group’ during P3 was significantly reduced compared with that during P1 (465±252 kcal, 37±15 g), whereas, EI and carbohydrate intake from the ‘supplements group’ of P3 was significantly increased compared with P1. The increased TrEE during P3 was not compensated by EI; instead, there was a decreased nutrient intake from the high-protein foods group and increased intake from the supplements group. The time of day of multiple or intensive training sessions, i.e. different TrEE, might affect the food choices made by male rugby players.