The expression of some proteins in the autophagy pathway declines with age, which may impact neurodegeneration in diseases, including Alzheimer’s Disease. We have identified a novel non-canonical function of several autophagy proteins in the conjugation of LC3 to Rab5+, clathrin+ endosomes containing β-amyloid in a process of LC3-associated endocytosis (LANDO). We found that LANDO in microglia is a critical regulator of immune-mediated aggregate removal and microglial activation in a murine model of AD. Mice lacking LANDO but not canonical autophagy in the myeloid compartment or specifically in microglia have a robust increase in pro-inflammatory cytokine production in the hippocampus and increased levels of neurotoxic β-amyloid. This inflammation and β-amyloid deposition were associated with reactive microgliosis and tau hyperphosphorylation. LANDO-deficient AD mice displayed accelerated neurodegeneration, impaired neuronal signaling, and memory deficits. Our data support a protective role for LANDO in microglia in neurodegenerative pathologies resulting from β-amyloid deposition. Display omitted •LC3-associated endocytosis (LANDO) requires Rubicon and ATG5, but not FIP200•LANDO is required for recycling of Aβ receptors including TREM2 in microglia.•LANDO confers protection against Aβ deposition and murine Alzheimer’s disease (AD)•Microglial LANDO protects against neuronal loss and memory impairment in murine AD An LC3-associated endocytosis pathway involved in the recycling of amyloid receptors is essential for the clearance of amyloid aggregates by microglia in a model of AD