Understanding the impact of technological and social entrepreneurship education on students’ critical thinking and innovation skills is crucial in adapting higher education to contemporary challenges. This study aimed to evaluate the effectiveness of a non-supervised algorithm for complex thinking profiling in strengthening these skills among university students. Using the eComplexity instrument, the study collected data from 1,071 participants in various disciplines, with pre-test and post-test evaluations. Clustering analysis was performed to identify response patterns, and the results were visualized using Principal Component Analysis (PCA). The key findings include: (a) Cluster 0 showed a significant decline in scientific and critical thinking skills, (b) Cluster 1 exhibited substantial improvement in critical and innovative thinking, (c) Cluster 2 demonstrated a decrease in scores despite initial high performance, and (d) differentiated instructional approaches are needed to address varied responses. The distinguishing value of this study lies in its implications for educational communities, societal development, and decision-makers, highlighting the need for tailored entrepreneurship education to promote sustainable innovation and societal progress.