Given the wide variety of conditioning program trainings employed, the present study compared the catabolic effects induced by CrossFit and resistance training in moderately trained subjects. Twenty males joined either the CrossFit group (n = 10; 30 min/day of "workout of the day") or the resistance training (RT) group (n = 10; 30 min/day of resistance exercises) thrice a week, for 8 weeks. Salivary levels of cortisol, interleukin 1-beta (IL-1β), and uric acid were assessed via enzyme-linked immunosorbent assays before (PRE) and 30-min after (POST) SESSION 1 and SESSION 24. Variables' percentual changes were computed as (POST-PRE)/PRE*100 in each session (Δ%). CrossFit acutely increased cortisol levels in both sessions, with a significant decrease in Δ%cortisol from SESSION 1 to 24. In the RT group, cortisol values decreased in both sessions, only acutely. A significant decrease in IL-1β levels was registered acutely in both groups, in both sessions, whereas Δ%IL-1β was not different between the two groups. While uric acid levels increased in both groups acutely, a chronic downregulation of Δ%uric acid, from SESSION 1 to 24, was appreciated for the RT group only. Overall, CrossFit appeared to induce more intense effects than the RT program as to the investigated catabolic responses.