We investigate the impact of preheating on baryogenesis in $R^2$-Higgs inflation. In this scenario, the inclusion of a dimension-six operator ${(R/ \Lambda^2)} B_{\mu\nu} \widetilde{B}^{\mu\nu} $ abundantly generates helical hypermagnetic fields during inflation, leading to a baryon asymmetric Universe at the electroweak crossover. Focusing on the $R^2$-like regime, we first derive the relevant dynamics of preheating using a doubly-covariant formalism. We find that preheating can happen for the Higgs, transverse gauge and Goldstone bosons, however, it is dependent on the value of the non-minimal coupling $\xi_H$ between the Standard Model Higgs field and the Ricci scalar. We identify the preheating temperature to determine the appropriate scale $\Lambda$ for driving baryogenesis, which is around $\Lambda \sim 2.2 \, (2.6) \times 10^{-5}\, M_{\rm P}$ for $\xi_H \sim 1 \, (10)$. Our results represent the most accurate estimation of the scale of gravity induced baryogenesis in $R^2$-Higgs inflation to date. Areas for further improvement are identified.