The aim of this work was to compare different approaches to VMAT optimization (biological vs. physical DVH-based) in two commercial treatment planning systems (TPS) for head and neck and prostate cases, using Pareto fronts. VMAT vs. IMRT Pareto front comparison was additionally performed in order to benchmark the optimizer efficiency and VMAT plan quality for each TPS. Three prostate and three head and neck cancer patients were selected for nine-beam IMRT and single-arc VMAT planning in Monaco 3.00 and Oncentra MasterPlan (OMP) 3.3 planning systems. Pareto fronts for prostate cases were constructed based on PTV coverage by 95% isodose and volume of rectum receiving 60 Gy or more. For head and neck cases, PTV coverage by the same isodose and mean dose to parotid gland were used for the construction of Pareto fronts. DVH analysis was performed together with evaluation of planning and delivery efficiency for all the plans. In the intersystem comparison for prostate plans, Monaco generated very similar IMRT and VMAT solutions. Quality of Monaco VMAT plans was superior compared to Oncentra in terms of conformity, homogeneity, and lower median dose to bladder due to biological formalism of optimization cost functions. For the head and neck cases, IMRT and VMAT plans were similar in both systems, except the case where a very strong modulation was required. In this situation single-arc VMAT plan generated with OMP was inferior compared to IMRT. VMAT OMP solutions were similar to Monaco or slightly better for two less-modulated head and neck cases. However, this advantage was achieved on the cost of lower conformity and homogeneity of the Oncentra VMAT plans. IMRT and VMAT solutions generated by Monaco were very similar for both prostate and head and neck cases. Oncentra system shows a bigger difference, and use of the dual-arc VMAT would be recommended to achieve the same plan quality as nine-field IMRT. Biological optimization seems beneficial in terms of plan conformity and homogeneity and allowed achieving lower OAR doses for prostate cases. In complex anatomical situations represented by head and neck cases, sequencing algorithm in Monaco imposed limitations on VMAT plan quality in the intersystem comparison.