Abstract Background Pain hypersensitivity can be assessed using Quantitative Sensory Testing (QST) and is associated with persistent low back pain. Spinal manipulation appears to modify pain hypersensitivity, and this could function as one mechanism leading to clinical improvements. In the current study, we applied a comprehensive QST battery to assess pain sensitivity in a cohort of low back pain patients before and after spinal manipulation to improve our understanding of the association between QST and clinical improvements. This study addresses two questions: Are clinical improvements following spinal manipulation in low back pain patients contingent on pain hypersensitivity, and does pain sensitivity change following spinal manipulation? Methods We performed a secondary analysis of data from a randomized clinical trial. One hundred and thirty-two participants with persistent LBP were treated with spinal manipulation four times over two weeks. Patient-reported outcomes and QST were assessed at baseline, after the fourth spinal manipulation session, and 14-days later. The clinical outcomes were changes in low back pain intensity and disability. Using latent profile analysis, we categorized the participants into clusters depending on their baseline QST scores. We used linear mixed models to examine the association between clusters and changes in patient-reported outcomes and QST. Results Two clusters emerged: a Sensitized and a Not sensitized. The former had significantly lower regional pressure and thermal pain thresholds, remote pressure pain tolerance, and lower inhibitory conditioned pain modulation than the Not sensitized group. However, we only found between-cluster differences for regional pressure pain threshold following spinal manipulation. Thus, the clusters were not associated with patient-reported pain and disability changes or the remaining QST outcomes. Conclusions We report that the baseline QST profile was not associated with clinical improvements following spinal manipulation. We did observe a substantial change for regional pressure pain threshold, which suggests that any effect of spinal manipulation on pain sensitivity is most likely to be observed as changes in regional, mechanical pain threshold. However, the mechanism that invokes clinical improvement and pain sensitivity changes appear distinct. Due to methodological caveats, we advise caution when interpreting the results. Trial registration Clinical.Trial.gov identifier: NCT04086667, registered 11 September 2019 – Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT04086667