Autophagy is a cellular survival and death pathway that is responsible for the degradation of cellular constituents such as long-lived proteins and organelles. Therefore, it is highly regulated by various signaling pathways including kinases including mTOR, AKT and AMPK, or transcription factors such as FOXO and p53. Moreover, cellular stress-inducers such as hypoxia or pathogen entry may activate autophagy. Therefore, pathways responding to various extracellular and intracellular cues might have an influence on autophagy regulation. Being a key biological event for homeostasis, dysregulation of autophagy was shown to play a role in pathologies such as cancer, myopathies and neurodegenerative diseases. In this context, development of small molecules or drugs modulating autophagy are important to correct defects in autophagy-related pathologies. In recent years, microRNAs arose as novel regulators of autophagy, and microRNAs networks targeting different autophagy-related proteins started to emerge. Here, we summarize the current knowledge on microRNA regulation of autophagy and introduce miRNA pathways as novel modulators of complex autophagy networks. Understanding the details of microRNA regulation of autophagy might also provide tools to better diagnose, follow and treat diseases developing due to autophagy abnormalities.