In the present study, an attempt is made to investigate and optimize the bead geometries of bead width (BW) and bead height (BH) of SS-309L using an SS316L substrate by employing a gas metal arc welding (GMAW)-based wire-arc additive manufacturing (WAAM) process. The Box–Behnken design approach was used to conduct the trials of single-layer depositions with input variables of travel speed (TS), voltage (V), and gas mixture ratio (GMR). The developed multi-variable regression models were tested for feasibility using ANOVA and residual plots. The data obtained indicated that V had the most significant impact on BW, followed by TS and GMR. For BH, TS had the most significant impact, followed by GMR and V. The results of single-response optimization using a passing vehicle search (PVS) algorithm showed a maximum BH of 9.48 mm and a minimum BW of 5.90 mm. To tackle the contradictory situation, a multi-objective PVS algorithm was employed, which produced non-dominated solutions. A multi-layered structure was successfully fabricated at the optimal parametric settings of TS at 20 mm/s, of voltage at 22 V, and of GMR at 3. For multi-layer structures, fusion among the layers was observed to be good, and they were found to be free from the disbonding of layers. This revealed the suitability of the PVS algorithm for generating suitable optimal WAAM variables. We consider the current work highly beneficial for users fabricating multi-layer structures.