Recent years have seen the proliferation of fused deposition modeling (FDM) as a means of manufacturing biodegradable products, for different applications such as rigid packaging, agricultural and biomedical. Blends of Polyhydroxyalkanoates (PHA) and polylactic acid (PLA) have been investigated to ascertain their prospective applications through FDM. This paper includes three parameters that affect the build process: layer height, nozzle temperature, and flow rate. 3D printed PLA/PHA can be characterized mechanically, and process parameters can be optimized to maximize design functionality. The experimental setup utilized a Taguchi L9 design, and TOSPIS was employed to optimize the output results. Using TOPSIS analysis, 0.2 mm layer thickness, 195 °C nozzle temperature, and 100 % flow rate were found to be the most optimal initiation parameters. The Taguchi analysis was used to analyze the output responses, and it was found that layer height had the greatest influence on mechanical properties, followed by flow rate and nozzle temperature. The percentage elongation at break has been improved significantly by adding PHA i.e., 170 % compared to PLA (5–10 %). This paper presents a framework for in-depth mechanical characterization of PLA-PHA 3D-printed parts, along with methods for optimizing process parameters to achieve optimal performance, as well as tools for modeling output responses using GA-ANN with an accuracy of 95 %.