Controlled plant crosses can be an important component of studies ranging from applied artificial selection research to evolutionary investigations of heritability. Controlling pollen flow is especially challenging for wind-pollinated species. We developed a system capable of housing hundreds of ragweed (Ambrosia artemisiifolia) plants simultaneously in individual chambers through the reproductive portion of their lifecycles. We confirmed that our chambers allowed us to control pollen movement and paternity of offspring using unpollinated isolated plants and microsatellite markers for parents and their putative offspring. Our system had per plant costs and efficacy superior to pollen bags used in past studies for wind pollinated plants. Our chamber system is flexible, affordable, and widely applicable to other wind pollinated plants, or applications in which the distribution of highly mobile species, individuals, spores, or gametes must be controlled.