To present the process undertaken by our institute in commissioning Mobius3D (M3D) for patient-specific quality assurance. 168 plans were randomly selected to compare dose distribution measured with ArcCheck and dose calculated from M3D, both compared against the treatment planning system (TPS). The gamma criteria for measurement and M3D are 3%/2mm with 10% and 50% dose thresholds, respectively. The effect of tissue inhomogeneity was investigated on 11 plans by recalculating the dose in M3D on a homogeneous phantom. Tolerance and action limits were established following the AAPM Task Group 218 recommendations. The M3D showed high variability in gamma passing rate compared to the measurement. Twenty-three out of 168 plans had false negative dose comparisons. These plans fall under high tissue inhomogeneity like lung and metal implants, small field targets, and breast plans planned with high energy. One false negative case (0.6%) was observed. A single tolerance limit of 91% and 92% gamma passing rate for the M3D and measurement-based PSQA were established, respectively. Against the expectation, recalculating plans on the homogeneous phantom in M3D did not necessarily increase the gamma passing rate. These plans have a duty cycle >4.2, and the small field sizes combined with differences in slice thickness contributed to observed dose differences in the homogeneous phantom comparisons. Following the commissioning, M3Dis adopted in our institute. Currently, the gamma criteria used for measurement and M3Dare 3%/2mm, 40% dose threshold, with gamma passing rates of 92% and 95%, respectively. A higher passing rate for M3D is adopted until more data is available. The combined effect of plan modulation, the field sizes, the tissue inhomogeneity, the dose algorithm, and the volume averaging effect from differences in slice thickness can contribute to the differences in dose in M3Dand TPS.