Appropriate selection of wire–arc additive manufacturing (WAAM) variables imparts bead geometries with characteristics of multi-layer structures. Thus, the present study aimed to optimize the gas metal arc welding (GMAW)-based WAAM variables of travel speed (TS), wire feed speed (WFS), and voltage (V) for the bead geometries of bead width (BW) and bead height (BH) on an SS 316L substrate. Single-layer depositions were made through a metallic wire of SS 316L by following an experimental matrix of the Box–Behnken design (BBD) technique. Multivariable regression equations were generated for design variables and responses, and ANOVA was used to investigate the feasibility of the obtained regression equations. WFS was the highest contributor affecting the BW, followed by V and TS, while WFS was again the highest contributor affecting the BH, followed by TS and V. Heat transfer search (HTS) optimization was used to attain optimal combinations. The single-objective optimization result showed a maximum bead height and minimum bead width of 6.72 mm and 3.72 mm, respectively. A multi-layer structure was then fabricated by considering an optimization case study, and it showed optimized parameters at a WFS of 5.50 m/min, TS of 141 mm/min, and voltage of 19 V with the bead height and bead width of 5.01 mm and 7.81 mm, respectively. The multi-layered structure obtained at the optimized parameter was found to be free from disbonding, and seamless fusion was detected between the obtained layers of the structure. The authors believe that the present study will be beneficial for industrial applications for the fabrication of multi-layer structures.