Differences in organization of the primary motor cortex and altered trunk motor control (sensing, processing and motor output) have been reported in people with low back pain (LBP). Little is known to what extent these differences are related. We investigated differences in 1) organization of the primary motor cortex and 2) motor and sensory tests between people with and without LBP, and 3) investigated associations between the organization of the primary motor cortex and motor and sensory tests. We conducted a case-control study in people with (N=25) and without (N=25) LBP. The organization of the primary motor cortex (Center of Gravity (CoG) and Area of the cortical representation of trunk muscles) was assessed using neuronavigated transcranial magnetic stimulation, based on individual MRIs. Sensory tests (quantitative sensory testing, graphaesthesia, two-point discrimination threshold) and a motor test (spiral-tracking test) were assessed. Participants with LBP had a more lateral and lower location of the CoG and a higher temporal summation of pain. For all participants combined, better vibration test scores were associated with a more anterior, lateral, and lower CoG and a better two-point discrimination threshold was associated with a lower CoG. A small subset of variables showed significance. Although this aligns with the concept of altered organization of the primary motor cortex in LBP, there is no strong evidence of the association between altered organization of the primary motor cortex and motor and sensory test performance in LBP. Focusing on subgroup analyses regarding pain duration can be a topic for future research.