Sensing based on Nitrogen‐Vacancy (NV) centers in nanodiamonds (NDs) represents a potentially groundbreaking technology with broad applications. Nevertheless, the optimization of their quantum‐optical properties is still a challenging issue. The present work aims at enhancing and controlling NV centers optical properties in NDs by combining their surface chemistry tuning and proton beam irradiation. Systematic thermal oxidations are carried out to study the evolution of surface chemical groups (IR spectroscopy), as well as their influence on optical properties (photoluminescence spectroscopy, PL decay measurements). Proton irradiation is performed by exploring a wide range of fluences (1014 – 1017 cm−2) in order to precisely control the amount of NV centers, thus defining the conditions that maximize their creation and emission intensity. In addition, NV centers charge state control is achieved by assessing NV−/NV0 ratio upon different surface termination tuning and NV centers amount. Finally, a novel predictive mathematical model is developed, allowing for the evaluation of the efficiencies of the formation of both NV− and NV0. Although the model is tested in the specific case study with proton irradiated NDs, it offers a broad applicability, thus representing a key landmark in the prediction of the outcome of ion‐beam‐based color centers generation in diamond.