Background: Pilates is among the best conservative management strategies for chronic low back pain. However, several variations of Pilates exist. This study aimed to investigate physical measures that would detect immediate changes after a brief session of Clinical Pilates exercises. Changes in self-reported clinical outcomes, pain and function were also evaluated. Methods: A prospective cohort study was conducted. Eighteen young adults with chronic low back pain participated in this study. Participants were assessed for pain and function subjectively, and hip/knee strength and trunk/hip flexibility objectively, followed by a session of Clinical Pilates assessment and exercises. After the exercises, the participants were immediately reassessed for pain, function, strength, and flexibility. Results: Trunk/hip flexibility showed statistically significant changes after exercise, which were measured with the sit-and-reach test (−3.44 cm, 95% CI [−5.10, −1.79], p < 0.001) and the finger-to-floor test (−6.29 cm [−9.51, −3.06], p = 0.001). Statistical significance was not found in detecting strength changes in hip extension, hip abduction, and knee extension. Changes in pain (1.56 points [0.83, 2.28], p < 0.001) and patient-specific functional scale (−1.52 points [−1.93, −1.10], p < 0.001) were also found after exercise. Conclusions: Trunk/hip flexibility measures detected physical changes after Clinical Pilates exercise, as well as self-reported pain and function outcomes, without reducing strength performance.