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Quantum-classical hybrid algorithms are emerging as promising candidates for near-term practical applications of quantum information processors in a wide variety of fields ranging from chemistry to physics and materials science. We report on the experimental implementation of such an algorithm to solve a quantum chemistry problem, using a digital quantum simulator based on trapped ions. Specifically, we implement the variational quantum eigensolver algorithm to calculate the molecular ground-state energies of two simple molecules and experimentally demonstrate and compare different encoding methods using up to four qubits. Furthermore, we discuss the impact of measurement noise as well as mitigation strategies and indicate the potential for adaptive implementations focused on reaching chemical accuracy, which may serve as a cross-platform benchmark for multiqubit quantum simulators.