Despite the central role of Aedes aegypti mosquitoes as vectors in outbreaks of human pathogenic viruses such as dengue virus, chikungunya virus, and Zika virus (ZIKV), little is known about their spatial proteome organization. Previous proteomic studies mainly relied on whole-body or single-tissue analyses, limiting the resolution needed to uncover tissue-specific molecular responses governing vector competence and viral transmission. Here, we present ProAedesDB, the first spatial proteomic atlas of naïve and ZIKV-infected Ae. aegypti mosquitoes. Using label-free quantitative mass spectrometry, we profiled more than 6,700 proteins across 13 anatomical compartments, including exoskeletal structures and internal organs such as salivary glands, midgut, and ovaries. Our analysis identified distinct tissue-specific protein signatures, selective markers, and functional enrichments. Comparative profiling with the widely used Aag2 and Aag2-C3 cell lines revealed protein-based tissue analogies, informing the physiological relevance of in vitro studies. Importantly, analysis of ZIKV-infected mosquitoes uncovered infection-driven host responses. Through RNAi-mediated silencing in vitro, we functionally assessed more than 100 dysregulated mosquito proteins, identifying a novel group of potent host factors regulating ZIKV replication. Finally, in vivo genetic approaches revealed a previously unknown host protein essential for efficient ZIKV transmission across multiple Ae. aegypti colonies. Taken together, these findings provide unprecedented insight into the tissue organization of the mosquito proteome and establish a molecular framework for studying vector biology and virus-host interactions at the organismal level. The dataset will be made publicly available through the ProAedesDB website, enabling discovery of molecular targets for vector control strategies.