Abstract Background In a prior randomized trial, we demonstrated that participants receiving spinal manipulative therapy at a pain-sensitive segment instead of a stiff segment experienced increased mechanical pressure pain thresholds. We hypothesized that the targeted segment mediated this increase through a segment-dependent neurophysiological reflective pathway. Presently, it is not known if this decrease in pain sensitivity is associated with clinical improvement. Therefore, we performed an explorative analysis to examine if changes in experimental pain sensitivity (mechanical and thermal) and lumbar stiffness were further dependent on clinical improvement in disability and patient-reported low back pain. Methods This study is a secondary explorative analysis of data from the randomized trial that compared 132 participants with chronic low back pain who received lumbar spinal manipulative therapy applied at either i) the stiffest segment or ii) the segment having the lowest pain threshold (i.e., the most pain-sensitive segment). We collected data at baseline, after the fourth session of spinal manipulation, and at 14-days follow-up. Participants were dichotomized into responders/non-responders using different clinical variables (disability and patient-reported low back pain) with varying threshold values (0, 30, and 50% improvement). Mixed models were used to assess changes in experimental outcomes (stiffness and pain sensitivity). The fixed interaction terms were time, segment allocation, and responder status. Results We observed a significant increase in mechanical pressure pain thresholds for the group, which received spinal manipulative therapy at the most pain-sensitive segment independent of whether they improved clinically or not. Those who received spinal manipulation at the stiffest segment also demonstrated increased mechanical pain sensitivity, but only in the subgroup with clinical improvement. We did not observe any changes in lumbar stiffness. Conclusion Our results suggest the existence of two different mechanistic pathways associated with the spinal manipulation target. i) A decrease of mechanical pain sensitivity independent of clinical outcome (neurophysiological) and ii) a decrease as a reflection of the clinical outcome. Together, these observations may provide a novel framework that improves our understanding of why some respond to spinal manipulative therapy while others do not. Trial registration ClinicalTrials.gov identifier: NCT04086667 registered retrospectively September 11th 2019.