This study aims to explore the process of entrepreneurial metacognition among founders of knowledge-based businesses. In terms of purpose, the research is applied in purpose and qualitative in implementation, with a descriptive and exploratory orientation. Data were collected through semi-structured interviews and analyzed using a thematic analysis approach. The statistical population consisted of founders of knowledge-based businesses at the Sistan and Baluchestan Science and Technology Park, and sampling continued until theoretical saturation was achieved (15 semi-structured interviews). Qualitative data were iteratively reviewed, analyzed, and structured using MAXQDA software (version 2024). The findings reveal a five-stage model comprising cognitive alert activation, fundamental assumption analysis, strategic reconstruction, emotional-cognitive monitoring, and pattern internalization. According to the results, founders of businesses, when confronted with signals from a high-stress environment, engage in redefining cognitive schemas and adjusting decision-making strategies through reflective self-awareness and remedial thinking. This process, supported by emotional-cognitive monitoring and the stabilization of reconstructed strategies, forms a self-reinforcing cycle that enhances cognitive resilience and mental flexibility. The validity of the model was confirmed using Lincoln and Guba’s qualitative criteria (credibility, dependability, transferability, and confirmability), along with an expert evaluation ratio test. Additionally, the calculated coefficients for test–retest reliability (0.83) and intra-subject agreement (0.72) verify the coherence of the coding procedures. The proposed model, while enriching the existing theoretical literature, provides a practical framework for designing educational and policy interventions in the domain of entrepreneurial metacognition within innovation ecosystems of less-developed regions.