Process optimization of photovoltaic devices is a time-intensive, trial-and-error endeavor, without full transparency of the underlying physics, and with user-imposed constraints that may or may not lead to a global optimum. Herein, we demonstrate that embedding physics domain knowledge into a Bayesian network enables an optimization approach that identifies the root cause(s) of underperformance with layer-by-layer resolution and reveals alternative optimal process windows beyond global black-box 2 optimization. Our Bayesian-network approach links process conditions to materials descriptors (bulk and interface properties, e.g., bulk lifetime, doping, and surface recombination) and device-performance parameters (e.g., cell efficiency), using a Bayesian inference framework with an autoencoder-based surrogate device-physics model that is 100x faster than numerical solvers. With the trained surrogate model, our approach is robust and reduces significantly the time-consuming experimentalist intervention, even with small numbers of fabricated samples. To demonstrate our method, we perform layerby-layer optimization of GaAs solar cells. In a single cycle of learning, we find an improved growth temperature for the GaAs solar cells without any secondary measurements, and demonstrate a 6.5% relative AM1.5G efficiency improvement above baseline and traditional black-box optimization methods.