Autophagy is a conserved lysosome-mediated pathway essential for cellular homeostasis, development, and stress responses. The fruit fly Drosophila melanogaster serves as a powerful model for autophagy research due to its genetic tractability and conservation of human disease genes. This chapter details fluorescence microscopy–based methods to monitor autophagy in multiple tissues, including the brain, midgut, Malpighian tubules, and ovary, under nutrient-replete and starvation conditions. Autophagosome dynamics are visualized using mCherry-Atg8a, while lysosomes are detected with CathepsinL immunostaining; colocalization of these markers in presence and absence of autophagy inhibitors can be used to measure autophagic flux. Clearance of Ref(2)P/p62 is additionally used as a readout for cargo degradation. Stepwise protocols are provided for tissue dissection, fixation, staining, and imaging, with guidance on data analysis and image processing. These approaches enable reproducible assessment of tissue-specific autophagy in vivo, offering valuable tools to investigate its roles in development, stress adaptation, and aging in Drosophila.