The MiniBooNE experiment has contributed substantially to beyond standard model searches in the neutrino sector. The experiment was originally designed to test theΔm2~1 eV2region of the sterile neutrino hypothesis by observingνe(ν-e) charged current quasielastic signals from aνμ(ν-μ) beam. MiniBooNE observed excesses ofνeandν-ecandidate events in neutrino and antineutrino mode, respectively. To date, these excesses have not been explained within the neutrino standard model (νSM); the standard model extended for three massive neutrinos. Confirmation is required by future experiments such as MicroBooNE. MiniBooNE also provided an opportunity for precision studies of Lorentz violation. The results set strict limits for the first time on several parameters of the standard-model extension, the generic formalism for considering Lorentz violation. Most recently, an extension to MiniBooNE running, with a beam tuned in beam-dump mode, is being performed to search for dark sector particles. This review describes these studies, demonstrating that short baseline neutrino experiments are rich environments in new physics searches.