A fundamental understanding of planetary histories and characteristics requires an empirical connection between planet formation and evolved planets—a long-sought goal of astrophysics. This connection is now increasingly possible due to simultaneous revolutions in the observations of protoplanetary disks and exoplanet atmospheres. A key step towards relating these observations of different evolutionary stages is to characterize the material in protoplanetary disks and relate these properties to the atmospheric properties of planets. I will discuss initial steps that I have taken towards this goal. I will provide evidence that protoplanetary disks are more than an order of magnitude more massive than previously appreciated, that the non-equilibrium processes of cloud formation and photochemistry shape substellar atmospheres, and that the physics of modeling clouds gives a new understanding of the compositional distribution in protoplanetary disks. Along the way, I will highlight novel opportunities for an unprecedented characterization of both atmospheres and disks. I will conclude by discussing avenues for relating planetary properties to the compositional inventory in protoplanetary disks in order to develop the observationally-validated framework required to relate evolved planets to planet formation.