Accurate neutrino-nucleus interaction modeling is an essential requirement for the success of the accelerator-based neutrino program. As no satisfactory description of cross sections exists, experiments tune neutrino-nucleus interactions to data to mitigate mis-modeling.  In this talk, I will discuss how the interplay between near detector tuning and cross section mis-modeling affects new physics searches. I will present two illustrative new physics scenarios, light sterile neutrinos and missing energy signatures, present the relevant experimental signatures with and without tuning, and discuss the prospects of identifying new physics.