In resource-constrained environments, such as low-power edge devices and smart sensors, deploying a fast, compact, and accurate intelligent system with minimum energy is indispensable. Embedding intelligence can be achieved using neural networks on neuromorphic hardware. Designing such networks would require determining several inherent hyperparameters. A key challenge is to find the optimum set of hyperparameters that might belong to the input/output encoding modules, the neural network itself, the application, or the underlying hardware. In this work, we present a hierarchical pseudo agent-based multi-objective Bayesian hyperparameter optimization framework (both software and hardware) that not only maximizes the performance of the network, but also minimizes the energy and area requirements of the corresponding neuromorphic hardware. We validate performance of our approach (in terms of accuracy and computation speed) on several control and classification applications on digital and mixed-signal (memristor-based) neural accelerators. We show that the optimum set of hyperparameters might drastically improve the performance of one application (i.e., 52–71% for Pole-Balance), while having minimum effect on another (i.e., 50–53% for RoboNav). In addition, we demonstrate resiliency of different input/output encoding, training neural network, or the underlying accelerator modules in a neuromorphic system to the changes of the hyperparameters.