The evidence for primary motor cortex reorganization in people with low back pain varies and is conflicting. Little is known about its association with motor and sensory tests, and recovery. We investigated primary motor cortex (re)organization and its associations with motor and sensory tests over time in people with (N = 25) and without (N = 25) low back pain in a longitudinal study with a 5-week follow-up. Participants with low back pain received physical therapy. Primary motor cortex organization, including the center of gravity and area of the cortical representation of trunk muscles, was evaluated using neuronavigated transcranial magnetic stimulation, based on individual magnetic resonance imaging. A motor control test (spiral tracking test) and sensory tests (quantitative sensory testing, graphaesthesia, and 2-point discrimination) were administered. Multivariate mixed models with a 3-level structure were used. In non-recovered participants, the center of gravity of longissimus L5 moved significantly anterior, and their temporal summation of pain decreased significantly more than in people without low back pain. The spiral tracking path length decreased significantly in participants without low back pain, which differed significantly from the increase in recovered participants. Significant associations were found between center of gravity and area with quantitative sensory tests and the spiral tracking test. We found a limited number of significant changes and associations over time, mainly related to longissimus L5. For some of these findings, no logical explanation seems currently available. Hence, it is unclear whether meaningful changes in cortical organization occur in people with low back pain over a 5-week period.