The disclosure describes various aspects related to enabling effective multi-qubit operations, and more specifically, to techniques for enabling parallel multi-qubit operations on a universal ion trap quantum computer. In an aspect, a method of performing quantum operations in an ion trap quantum computer or trapped-ion quantum system includes implementing at least two parallel gates of a quantum circuit, each of the at least two parallel gates is a multi-qubit gate, each of the at least two parallel gates is implemented using a different set of ions of a plurality of ions in a ion trap, and the plurality of ions includes four or more ions. The method further includes simultaneously performing operations on the at least two parallel gates as part of the quantum operations. A trapped-ion quantum system and a computer-readable storage medium corresponding to the method described above are also disclosed.