Objectives Although motor control exercises have been shown to be effective in the management of low back pain (LBP) the mechanism of action is unclear. The current study investigated the relationship between the ability to recruit transversus abdominis and clinical outcomes of participants in a clinical trial. Methods Ultrasonography was used to assess the ability to recruit transversus abdominis in a nested design: a sample of 34 participants with chronic LBP was recruited from participants in a randomised controlled trial comparing the efficacy of motor control exercise, general exercise and spinal manipulative therapy. Perceived recovery, function, disability and pain were also assessed. Results Participants with chronic LBP receiving motor control exercise had a greater improvement in recruitment of transversus abdominis (7.8%) than participants receiving general exercise (4.9% reduction) or spinal manipulative therapy (3.7% reduction). The effect of motor control exercise on pain reduction was greater in participants who had a poor ability to recruit transversus abdominis at baseline. There was a significant, moderate correlation between improved recruitment of transversus abdominis and a reduction in disability (r = 20.35; 95% CI 0.02 to 0.62). Conclusion These data provide some support for the hypothesised mechanism of action of motor control exercise and suggest that the treatment may be more effective in those with a poor ability to recruit transversus abdominis.