Background: This study explores the potential of discarded male layer embryos as a sustainable and non-GMO cell source for cultivated chicken meat production. The research aims to identify efficient methods for isolating muscle progenitor cells (MPCs) with high proliferative potential by conducting transcriptome analysis on thigh muscle tissues from both male and female chick embryos. Methods: Transcriptome analysis was performed on the thigh muscle tissues of male and female chick embryos, aged 12-13 days, (n = 4 each), to investigate the gene expression profiles and identify strategies for efficiently isolating MPCs. This approach aims to pinpoint techniques that would allow for the selection of MPCs with optimal growth and proliferation capabilities. Results: Using heatmap, hierarchical clustering, and multidimensional scaling (MDS), we found no significant sex-based differences in gene expression, except for the overexpression of the female-specific gene LIPBLL. The expression of muscle stem cell factors, including PAX3, PAX7, and other myogenic regulatory genes, showed no significant variation. However, to recover MPC-rich cells isolated from male thigh muscle, we found that by the pre-plating 7 stage, myogenesis-related genes, MYHs and MUSTN1 were minimally expressed, while the cell cycle arrest gene CDKN1A sharply increased. Conclusions: Our findings suggest that simple cell isolation directly from tissue is a more scalable and efficient approach for cultivated meat production, compared to labor-intensive pre-plating methods, making it a viable solution for sustainable research and resource recycling.