Objective. Motor neuroprostheses require the identification of stimulation protocols that effectively produce desired movements. Manual search for these protocols can be very time-consuming and often leads to suboptimal solutions, as several stimulation parameters must be personalized for each subject for a variety of target motor functions. Here, we present an algorithm that efficiently tunes peripheral intraneural stimulation protocols to elicit functionally relevant distal limb movements. Approach. We developed the algorithm using Bayesian optimization (BO) with multi-output Gaussian Processes (GPs) and defined objective functions based on coordinated muscle recruitment. We applied the algorithm offline to data acquired in rats for walking control and in monkeys for hand grasping control and compared different GP models for these two systems. We then performed a preliminary online test in a monkey to experimentally validate the functionality of our method. Main results. Offline, optimal intraneural stimulation protocols for various target motor functions were rapidly identified in both experimental scenarios. Using the model that performed best, the algorithm converged to stimuli that evoked functionally consistent movements with an average number of actions equal to 20% of the search space size in both the rat and monkey animal models. Online, the algorithm quickly guided the observations to stimuli that elicited functional hand gestures, although more selective motor outputs could have been achieved by refining the objective function used. Significance. These results demonstrate that BO can reliably and efficiently automate the tuning of peripheral neurostimulation protocols, establishing a translational framework to configure peripheral motor neuroprostheses in clinical applications. The proposed method can also potentially be applied to optimize motor functions using other stimulation modalities.