Objective: To compare radiological measurements of the patellofemoral joint (PFJ) morphology and measurement reproducibility across the following scanning modalities: (a) 3 T supine MRI, (b) 0.25 T supine MRI and (c) standing 0.25 T MRI. Methods: Forty patients referred to MRI of the knee were scanned by high field 3 T MRI in supine position and low field 0.25 T positional (pMRI) in supine and standing positions. Radiological measurements for assessment of femoral trochlear morphology, patellar tracking, patellar height and knee flexion angle were compared across scanning situations by one-way repeated-measures ANOVA. Measurement reliability and agreement were assessed by calculation of ICC, SEM and MDC. Results: Patellar tracking differed across scanning situations, particularly between 3.0 T supine and 0.25 T standing position. Mean differences are the following: patella bisect offset (PBO): 9.6%, p ≤ 0.001; patellar tilt angle (PTA): 3.1°, p ≤ 0.001; tibial tuberosity-trochlear groove distance (TT-TG): 2.7 mm, p ≤ 0.001). Measurements revealed slight knee joint flexion in supine and slight hyperextension in the standing position (MD: 9.3°, P ≤ 0.001), likely related to the observed differences in patellar tracking. Reproducibility was comparable across MRI field strengths. In general, PBO, PTA and TT-TG were the most robust measurements in terms of reproducibility and agreement across scanning situations (ICC range: 0.85–0.94). Conclusion: Significant differences in important patellofemoral morphology measurements were observed between supine and standing MRI scanning positions. These were unlikely due to physiological factors such as changes in joint loading but rather induced by slight differences in knee flexion angle. This emphasises the need to standardise knee positioning during scanning, particularly for weight-bearing positional MRI before clinical use.