Little is known about the patterns and influences of physical activity change in mid-aged adults. This study describes the design, sampling, data collection, and analytical plan of HABITAT, an innovative study of (i) physical activity change over five years (2007–2011) in adults aged 40–65 years at baseline, and (ii) the relative contribution of psychological variables, social support, neighborhood perceptions, area-level factors, and sociodemographic characteristics to physical activity change. HABITAT is a longitudinal multi-level study. 1625 Census Collection Districts (CCDs) in Brisbane, Australia were ranked by their index of relative socioeconomic disadvantage score, categorized into deciles, and 20 CCDs from each decile were selected to provide 200 local areas for study inclusion. From each of the 200 CCDs, dwellings with individuals aged between 40–65 years (in 2007) were identified using electoral roll data, and approximately 85 people per CCD were selected to participate (N = 17,000). A comprehensive Geographic Information System (GIS) database has been compiled with area-level information on public transport networks, footpaths, topography, traffic volume, street lights, tree coverage, parks, public services, and recreational facilities Participants are mailed a questionnaire every two years (2007, 2009, 2011), with items assessing physical activity (general walking, moderate activity, vigorous activity, walking for transport, cycling for transport, recreational activities), sitting time, perceptions of neighborhood characteristics (traffic, pleasant surroundings, streets, footpaths, crime and safety, distance to recreational and business facilities), social support, social cohesion, activity-related cognitions (attitudes, efficacy, barriers, motivation), health, and sociodemographic characteristics. Analyses will use binary and multinomial logit regression models, as well as generalized linear latent growth models. HABITAT will provide unique information to improve our understanding of the determinants of physical activity, and to help identify "people" and "place" priority targets for public policy and health promotion aimed at increasing physical activity participation among mid-aged men and women.