The red-eared slide turtle (Trachemys scripta elegans) is able to survive prolonged episodes of anoxia without suffering any apparent damage. This feat is underscored by a complex set of regulatory mechanisms to achieve metabolic rate depression (MRD) including microRNA (miRNA)-mediated gene silencing. Immunoblotting of relative protein abundance was used to analyze miRNA biogenesis under anoxic and reoxygenated conditions in liver and muscle, finding tissue-specific regulation of miRNA production. Cytoplasmic granule proteins were also assessed to inspect mRNA fate, the results of which indicated that mRNA sequestration to stress granules or processing bodies was also tissue specific. Next, the miRNAome was analyzed using RNA sequencing and bioinformatic analyses, revealing anoxia-induced suppression of processes associated with cell cycle progression and protein turnover. Altogether, these results indicate that miRNA targeting of mRNA transcripts occurs in a tissue specific manner with a particular focus on the suppression of energetically expensive processes.