This study examined the challenges encountered in the operational expenditure process of the School-Based Feeding Program (SBFP) among elementary schools in the San Manuel District, Pangasinan, during School Year 2025–2026. Specifically, the study determined the profile of participating schools, assessed the degree of operational challenges in planning, budgeting, purchasing and compliance, validation, and reporting, and identified significant differences among schools regarding operational expenditure practices. The study also proposed management enhancement measures to improve SBFP implementation. A descriptive-comparative research design was employed. Data were collected from seventy-three (73) respondents composed of school heads, administrative officers, project development officers, and coordinators through a researcher-made questionnaire. Statistical tools used included frequency, percentage, weighted mean, and Analysis of Variance (ANOVA). Findings revealed that schools commonly experienced budgeting difficulties due to fluctuating market prices and challenges in maintaining standard meal costs. Reporting and validation issues included repeated corrections in liquidation reports, delayed submissions, and incomplete documentation. Procurement compliance challenges were associated with PhilGEPS procedures and technical limitations. The study concluded that operational expenditure concerns are systemic and require district-wide interventions focusing on financial management, reporting efficiency, procurement systems, and personnel capability enhancement.