The chemistry of indoor surfaces, and the role of microbes in shaping and responding to that chemistry, are largely unexplored. We found that over one month, people’s presence and activities profoundly reshaped the chemistry of a house. Molecules associated with eating/cooking, bathroom use, and personal care were found throughout the entire house, while molecules associated with medications, outdoor biocides, and microbially-derived compounds were distributed in a location-dependent manner. The house, and its microbial occupants, in turn, also introduced chemical transformations such as oxidation and transformations of foodborne molecules. The awareness of and the ability to observe the molecular changes introduced by people should influence future building designs.