The total food waste constitutes a great portion of perishable goods and Kaya (2021) stated that inventory management has been proven to be more challenging for perishable goods since these deteriorate over time and become obsolete. This study will be significant for business owners in Convenience Store X in Marikina City and for future studies to have an effective inventory management. The objective of this study is to create user-focused inventory management system using a design thinking approach which is a five-stage process: Empathize, Define, Ideate, Prototype, Test. With that, the researchers gathered data and determined the users’ pain points related to the inventory management system for perishable goods in Convenience Store X. Then, the researchers came up with criteria and solutions for the new inventory system with the use of Multi-Criteria Decision Analysis (MCDA), specifically Analytical Hierarchy Process (AHP) and integrated with software developers in designing the three (3) user interfaces of a Software-as-a-service (SaaS) inventory system namely: System X, System Y and System Z. Through the Pugh Selection and User Acceptance Test, the researchers collected ratings from the users and concluded that System X is the most preferred design based on the users’ pain points and preferences.