The objective of this study was to evaluate the procedures for patient-specific quality assurance measurements using modulated scanned and energy stacked beams for proton and carbon ion teletherapy. Delivery records from 1734 portal measurements were analyzed using a 3-point pass criteria: more than 22 of 24 chambers in a water phantom (WP) had to have a measured dose difference from the planned portal doses less than or equal to 3%, or the distance from the measurement point location to a point location in the plan having the same dose had to be less than or equal to 3 mm (distance to agreement [DTA]), and the mean dose deviation of all chambers had to be less than 3%. Stratification of results showed some associations between measurement parameters and pass rates. For proton portals, pass rates were high at all measurement depths, but for carbon ion portals, pass rates decreased as a function of increasing measurement depth. Pass rates of both proton and carbon ion portals with 1 WP were slightly lower than those with a second WP. The total pass rates were 97.7% and 91.9% for proton and carbon ion patient portals, respectively. In general, the measured doses exhibited good agreement with the treatment planning system (TPS) calculated doses. When the chamber position was deeper than 150 mm in carbon ion beams, a lower pass rate was observed, which may have been caused by ion chamber array setup uncertainty (lateral and depth) in highly modulated portals or incorrect modeling of scatter by the TPS. These deviations need further investigation.