Although complex inflammatory-like alterations are observed around the amyloid plaques of Alzheimer’s disease (AD), little is known about the molecular changes and cellular interactions that characterize this response. We investigate here, in an AD mouse model, the transcriptional changes occurring in tissue domains in a 100-μm diameter around amyloid plaques using spatial transcriptomics. We demonstrate early alterations in a gene co-expression network enriched for myelin and oligodendrocyte genes (OLIGs), whereas a multicellular gene co-expression network of plaque-induced genes (PIGs) involving the complement system, oxidative stress, lysosomes, and inflammation is prominent in the later phase of the disease. We confirm the majority of the observed alterations at the cellular level using in situ sequencing on mouse and human brain sections. Genome-wide spatial transcriptomics analysis provides an unprecedented approach to untangle the dysregulated cellular network in the vicinity of pathogenic hallmarks of AD and other brain diseases. Display omitted •Spatial transcriptomics identifies a plaque-induced gene (PIG) network•Spatial transcriptomics identifies an oligodendrocyte gene (OLIG) response in AD•In situ sequencing in mouse and human confirms these responses at single-cell level•PIG and OLIG responses are conserved over different neurodegenerative diseases A combination of spatial transcriptomics and in situ sequencing on mouse and human brain demonstrates multicellular gene co-expression networks in Alzheimer’s disease, two of which are induced by accumulating amyloid plaques. A plaque-induced gene (PIG) network mainly involving micro- and astroglia and an oligodendrocyte gene (OLIG) and myelination response are identified.