The notion of universal quantum computation can be generalized to multilevel qudits, which offer advantages in resource usage and algorithmic efficiencies. Trapped ions, which are pristine and well-controlled quantum systems, offer an ideal platform to develop qudit-based quantum information processing. Previous work has not fully explored the practicality of implementing trapped-ion qudits accounting for known experimental error sources. Here, we describe a universal set of protocols for state preparation, single-qudit gates, a generalization of the Mølmer-Sørensen gate for two-qudit gates, and a measurement scheme which utilizes shelving to a metastable state. We numerically simulate known sources of error from previous trapped-ion experiments, and show that there are no fundamental limitations to achieving fidelities above 99% for three-level qudits encoded in 137 Ba + ions. Our methods are extensible to higher-dimensional qudits, and our measurement and single-qudit gate protocols can achieve 99% fidelities for five-level qudits. We identify avenues to further decrease errors in future work. Our results suggest that three-level trapped-ion qudits will be a useful technology for quantum information processing.