This dissertation focuses on observing and controlling cold atom-ion collisions. Such collisions have numerous applications ranging from providing insight into the formation of the interstellar medium to presenting a potential platform for developing quantum information architectures. The experimental apparatus at the center of this work is a hybrid atom-ion trapping system in which laser-cooled Ca atoms held within a magneto-optical trap are spatially overlapped with ions localized within an ion trap. The ions studied in this work are both laser-cooled atomic ions as well as sympathetically cooled molecular ions. As detailed in the remainder of this thesis, by employing tools such as optical pumping, collision energy control, and mass spectrometry, reactions between these species can not only be studied with high precision but can also be controlled, leading to expanded tools for reaction engineering as well as the creation of exotic chemical species. Finally, this work also includes efforts to use inelastic collisions between room temperature BaCl^+} molecular ions and cold Ca atoms to create ro-vibrational ground state molecules, a precursor for developing a high-fidelity qubit based on rotational levels in polar molecules.