Effective management of organizational processes and addressing challenges to achieve goals in today’s competitive world is vital for institutions such as the Cooperative Investment Guarantee Fund. The importance of this issue for the Fund is further amplified given its wide range of stakeholders and its key role in supporting the cooperative sector. Enhancing efficiency in such organizations requires continuous process improvement to reduce costs and time, increase effectiveness, and achieve stakeholder satisfaction. Accordingly, the present study was designed in three steps with the aim of identifying challenges and proposing improvement strategies. Grounded in the principles of quality management and process-oriented approaches, the study ensures the scientific validity and practical applicability of its results. The first and second steps focused on comprehensive identification and understanding of the current state of processes across all units to provide a complete picture of organizational performance. The methodology employed in these phases included drafting the project charter, conducting specialized training workshops, and collecting extensive data through expert interviews and document analysis, ultimately leading to process modeling based on the BPMN 2.0 standard. In the third step, an in-depth analysis of challenges and their prioritization was carried out using Multi-Criteria Decision-Making (MCDM), the TOPSIS technique, and the Nominal Group Technique (NGT). The findings revealed that the Fund’s major deficiencies are concentrated in the areas of process and strategy. Accordingly, optimization solutions were proposed in line with the extracted priorities, and Key Performance Indicators (KPIs) were developed for continuous monitoring. The final results of this study, in addition to creating process transparency, provide a practical and scientific roadmap that enables resource concentration on critical success factors—representing a pivotal step toward reducing time and cost, enhancing effectiveness, and achieving the Fund’s strategic objectives in the cooperative sector