Solar wind protons can interact directly with the hydrogen corona of Mars through charge exchange, resulting in energetic neutral atoms (ENAs) able to penetrate deep into the upper atmosphere of Mars. ENAs can undergo multiple charge changing interactions, leading to an observable beam of penetrating protons in the upper atmosphere. We seek to characterize the behavior of these protons in the presence of magnetic fields using data collected by the Mars Atmosphere and Volatile EvolutioN spacecraft. We find that backscattered penetrating proton flux is enhanced in regions where the magnetic field strength is greater than 200 nT. We also find a strong correlation at CO2 column densities less than 5.5 × 1014 cm−2 between magnetic field strength and the observed backscattered and downward flux. We do not see significant changes in penetrating proton flux with magnetic field strengths on the order of 10 nT. Plain Language Summary: Positively charged particles in the solar wind can directly interact with hydrogen in the Martian environment. These positively charged particles can charge exchange with hydrogen atoms, becoming fast, neutral atoms that are able to navigate their way deep into the upper atmosphere of Mars. These fast neutrals can undergo further charge‐changing reactions and become positively charged once more. This paper seeks to understand how these positive particles, or penetrating protons, behave in the presence of magnetic fields using data collected by the Mars Atmosphere and Volatile EvolutioN spacecraft. We find that strong magnetic fields enhance the number of backscattered penetrating protons we observe. At low atmospheric column densities, strong magnetic fields significantly deflect these protons back to higher altitudes. At high atmospheric column densities, magnetic fields do not appear to affect these penetrating protons to the same degree as collisions with other neutral molecules. We also find that small magnetic field strengths do not affect the penetrating proton flux we observe. Key Points: Backscattered penetrating proton flux is enhanced in magnetic field regions with strengths greater than 200 nTPenetrating protons are influenced by strong magnetic fields at column densities less than 5.5 × 1014 cm−2Penetrating proton fluxes are not greatly affected by magnetic field strengths on the order of 10 nT [ABSTRACT FROM AUTHOR]