Neutrino-nucleus cross sections are an important facet of interpreting results in accelerator neutrino experiments. However, these cross sections are still not theoretically well understood. In this talk, I will discuss how near detector tunes, widely adopted in accelerator neutrino experiments to address cross section uncertainties in oscillation analyses, affect new physics searches. I will present two illustrative new physics scenarios, light sterile neutrinos and missing energy signatures, present the relevant observable spectra before and after tune, and discuss the prospects of identifying new physics.