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It is well established that cells communicate with each other via signaling molecules and pathways. Recent work has further indicated that this transfer of information can breach the soma-to-germ line barrier, thus permitting changes in germline gene expression in response to cellular decisions made in somatic lineages. We show that during periods of extended energy stress AMPK alters small RNA biogenesis in somatic cells, which non-autonomously regulates the quiescence of germline stem cells. By combining both genetic analyses and a novel method of miRNA imaging, we show that AMPK-mediated phosphorylation acts as a molecular switch that drives the re-allocation of the key RNA endonuclease Dicer to the miRNA synthesis pathway during the dauer stage of C. elegans . By modifying Dicer and other components of the miRNA synthesis machinery, AMPK fine-tunes the production of a population of somatic miRNAs that act as a “pro-quiescence” signal to maintain germline integrity during periods of extended energy stress, thus bridging the gap between the soma and the germ line by altering small RNA homeostasis.