MicroRNAs are post-transcriptional regulators that play critical roles in diverse biological processes.We hypothesize that miRNAs may be involved in regulating transcriptome responses to changes inembryonic incubation temperature in chickens afecting diferentiation and proliferation processesduring tissue development. Therefore, we conducted comparative transcriptome profling of miRNAsto examine altered expression in breast and hind muscle of embryos and day 35 chickens experiencinghigh (38.8°C), control (37.8°C), or low (36.8°C) embryonic incubation temperature during embryonicday (ED) 7–10 or ED10–13. The results revealed diferential expression of miRNAs due to modifcationof embryonic incubation temperature in a muscle type-specifc and a developmental stage-specifcmanner. The immediate efects of thermal change observed in embryos were substantial comparedto the subtle long-term efects in chickens at day 35 post-hatch. Upregulation of miR-133 in breastmuscle and downregulation of miR-199a-5p, miR-1915, and miR-638 in hind muscle post ED7–10high-temperature treatment are functionally associated with myogenesis and body size. ED10–13low-temperature treatment led to downregulation of let-7, miR-93, and miR-130c that are related toproliferation and diferentiation. The results provide insight into the dynamics of miRNA expressionat variable embryonic incubation temperatures during developmental processes and indicate amajor regulatory role of miRNAs in acute responses to modifed environmental conditions that afectremodelling of cells and tissues.