INTRODUCTION: Using a single-nucleus transcriptome derived from the dorsolateral prefrontal cortex of 424 Religious Orders Study and the Rush Memory and Aging Project (ROS/MAP) participants, we investigated the cell type-specific effect of ten vascular endothelial growth factor (VEGF) genes on Alzheimer's disease (AD) endophenotypes. METHODS: Negative binomial mixed models were used for differential gene expression and association analysis with AD endophenotypes. VEGF-associated intercellular communication was also profiled. RESULTS: Higher microglia FLT1, endothelial FLT4, and oligodendrocyte VEGFB are associated with greater amyloid beta (Aβ) load, whereas higher VEGFB expression in inhibitory neurons is associated with lower Aβ load. Higher astrocyte NRP1 is associated with lower tau density. Higher microglia and endothelial FLT1 are associated with worse cognition performance. Endothelial and microglial FLT1 expression was upregulated in clinical AD patients compared to cognitively normal controls. Finally, AD cells showed a significant reduction in VEGF signaling compared to controls. DISCUSSION: Our results highlight key changes in VEGF receptor expression in endothelial and microglial cells during AD, and the potential protective role of VEGFB in neurons. HIGHLIGHTS: The prefrontal cortical expression of FLT1 and FLT4 was associated with worse cross-sectional global cognitive function, longitudinal cognitive trajectories, and more Alzheimer's disease (AD) neuropathology. The associations between FLT1 or FLT4 and AD endophenotypes appear to be driven by endothelial and microglial cells. VEGFB expression seems to have opposing effects on the Aβ burden in AD depending on cell types, highlighting its potential protective role in neurons.