Arthrogenous muscle inhibition (AMI) is thought to contribute to quadriceps weakness in knee osteoarthritis (OA), but its relationship with structural changes of bone marrow lesions (BMLs), capsular distension and pain is unclear. This study's objective was to investigate the factors associated with AMI in subjects with symptomatic patellofemoral joint OA (PFJOA). 126 Subjects with predominant PFJOA were assessed for pain by the visual analogue scale (VAS) for a nominated aggravating activity. Their more symptomatic knee underwent amagnetic resonance imaging (MRI) scan which was used to assess BMLs and synovitis which were scored using the Whole Organ MRI score (WORMS). Quadriceps AMI was measured by calculating the activation deficit and quadriceps strength assessed by isometric maximum voluntary contraction. Multiple linear regressions were used to assess factors associated with AMI. We studied 124 subjects [mean age 55.5 (SD 7.5); 57.14% female]. In regression analyses, higher levels of AMI were significantly associated with more severe knee pain and with lower BML score. Quadriceps AMI in knee OA is associated with severity of knee pain and surprisingly with lower BML scores.