One of the most fundamental concerns of policymakers and stakeholders is finding a solution to the unemployment crisis. This issue is particularly critical in the agricultural sector, where it has significantly reduced the resilience of agricultural colleges. Establishing and developing an entrepreneurial ecosystem facilitates the transformation of universities into entrepreneurial, third-generation universities. Identifying the components of the university’s entrepreneurial ecosystem plays a crucial role in recognizing entrepreneurial opportunities and improving the entrepreneurial resilience of universities. The present study aims to identify the factors influencing the resilience of agricultural colleges to improve skill-based education and enhance the employability of undergraduate students, with an emphasis on the pivotal role of the entrepreneurial ecosystem. This quantitative, descriptive research was conducted using a survey method and stratified random sampling among 214 students. Data were collected through a questionnaire, whose validity was confirmed by experts and reliability established via a pilot study and Cronbach’s alpha coefficient. To analyze the data and test the causal model, path analysis was performed using AMOS software. The findings of the causal model reveal that creating an entrepreneurial ecosystem and fostering entrepreneurial activities have a direct, positive, and significant impact on the resilience of entrepreneurial education in agricultural colleges. Internal networking, external networking, and organizational integration also have a direct, positive, and significant effect on the resilience of agricultural colleges. Institutionalizing the entrepreneurial process in universities not only helps address the unemployment challenges of graduates but also fosters the creation of innovative ideas. Institutionalizing entrepreneurship in universities leads to job creation, wealth generation, improved living standards, and ultimately, the country’s overall development. Therefore, by establishing a suitable entrepreneurial ecosystem, universities can cultivate creative innovators and take essential steps toward becoming third-generation universities.