<p>Understanding cellular biomechanics through embryo mechanophenotyping provides critical insights into cellular functions and disease mechanisms and is important for advancing biomedical research and therapeutic innovations. This paper presents a minimally invasive and non-prehensile magnetic microrobotic system for a comprehensive biomechanical analysis of zebrafish embryos. We developed a specialized suction-based technique for immobilizing live embryos, integrating it with a customized Petri dish, significantly enhancing embryo handling efficiency and increasing experimental throughput. The technique was complemented by an image-guided localization, which accurately identified and tracked the microrobot and embryos within the workspace, further enhancing the efficiency and reliability of mechanophenotyping. The developed microrobotic system overcomes challenges like tethered actuation and potential cell damage seen with other tools. Our microrobotic mechanophenotyping reliably captured the developmental trend of Young’s modulus, peaking at the blastula stage and decreasing toward hatching, consistent with known observations of chorion softening. The system continuously measured biomechanical changes for 8&#xa0;hours without compromising embryo viability, confirming its minimally invasive nature. With a survival rate of 88.88% post measurements, this tool offers a minimally invasive and effective alternative for biomechanical profiling, providing key insights into embryonic development and laying the foundations for future research on mechanical forces in embryogenesis.</p>