In this study, a sustainable protocol for PHA extraction was methodically selected using two (2) multi-criteria decision analysis (MCDA) tools, the analytic hierarchy process (AHP) and grey relational analysis (GRA). AHP was first used to evaluate the proposed criteria categorized into technical, economic, and environmental aspects using a collected survey of pairwise comparisons. Based on the results of AHP, it was identified that both environmental and economic aspects were given higher priorities. Among the criteria, hazards and risks has the highest overall importance, followed by extraction cost and purity. Using GRA, twelve (12) protocol alternatives categorized into solvent extraction and precipitation, non-PHA cell mass (NPCM) digestion, and assisted extraction methods were graded according to the criteria. Overall, the highest priority weights were given to NPCM digestion protocols including sodium hydroxide, sodium hydroxide + sodium dodecyl sulfate, and ammonia water. The reagents involved in these protocols are ecologically benign and cheaper compared to other solvents; hence, the higher grades in the environmental and economic aspect. Sensitivity analysis also proved that these protocols are excellent, particularly if extraction cost is given a higher priority. However, if hazards and risks and purity were given more importance, butyl acetate is preferable than sodium hydroxide. Further investigations such as the validation and optimization of protocols, together with feasibility studies and life cycle analyses may be integrated with the results of this study to comprehensively determine a sustainable PHA extraction protocol.