Physical activity (PA) is recommended as a primary treatment to reduce pain and improve function in chronic low back pain (cLBP). However, adherence to PA guidelines and the limitation of sedentary behavior (SB) remain challenging for cLBP patients. While some studies focus on PA promotion, past results are mixed, and the role of SB has not been thoroughly investigated. This observational study aims to assess changes in PA and SB levels among cLBP patients participating in a rehabilitation program (RP) and explore related changes in both explicit and implicit motivational factors. Patients wore an accelerometer for 1 week before the RP (T1) and 3 months afterward (T4) to measure PA and SB. At the start (T2) and at the end (T4) of the RP, we measured motivation, including implicit attitudes, toward these two behaviors. Between T1 and T4 (n = 33), the results show a significant decrease in SB. Between T2 and T3 (n = 62), all motivational variables were significantly more in favor of an active lifestyle, but implicit attitudes did not significantly change. This study shows that an RP can transform behavior determinants and reduce SB but is less efficient to increase PA levels. It also emphasizes the need to work with patients to enhance adherence and objectively measure behaviors in the future.