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Within the agri-food industry, substantial quantities of by-products are generated during the collection of raw materials and the preparation of derived food products. A common by-product is the low-value substandard bean that might have structural damages but retains its nutritional characteristics. This research aimed to evaluate the compatibility of bean protein with corn flour starch within an extruded snack model through molecular dynamics simulation by the calculation of the solubility parameter (δ). For the extrusion processing, a central composite design was used with four factors: temperature [150–190 °C], screw speed [150–210 rpm], moisture content [14–18%] and substandard bean content [20–80%]. Simulation calculations were performed using Materials Studio 8.0 software (Accelrys, San Diego, CA). The bean protein was identified as ARC5A, and its structure was obtained from the UniProt database. Starch and protein models evaluated within a temperature profile [25–150 °C] emulating the extrusion processing showed Δδ < 7.0 MPa0.5, indicating that are likely miscible. Optimal processing conditions of the extruded snack were obtained. This research developed an extruded snack using an agro-industrial by-product while predicting the solubility and miscibility parameters of more compounds using molecular dynamics simulations.