We describe a new, more accurate procedure for estimating and removing inner zone background contamination from Van Allen Probes Magnetic Electron Ion Spectrometer (MagEIS) radiation belt measurements. This new procedure is based on the underlying assumption that the primary source of background contamination in the electron measurements at L shells less than three, energetic inner belt protons, is relatively stable. Since a magnetic spectrometer can readily distinguish between foreground electrons and background signals, we are able to exploit the proton stability to construct a model of the background contamination in each MagEIS detector by only considering times when the measurements are known to be background dominated. We demonstrate, for relativistic electron measurements in the inner zone, that the new technique is a significant improvement upon the routine background corrections that are used in the standard MagEIS data processing, which can “overcorrect” and therefore remove real (but small) electron fluxes. As an example, we show that the previously reported 1‐MeV injection into the inner zone that occurred in June of 2015 was distributed more broadly in L and persisted in the inner zone longer than suggested by previous estimates. Such differences can have important implications for both scientific studies and spacecraft engineering applications that make use of MagEIS electron data in the inner zone at relativistic energies. We compare these new results with prior work and present more recent observations that also show a 1‐MeV electron injection into the inner zone following the September 2017 interplanetary shock passage. Plain Language Summary All measurements suffer from error, which can arise from a variety of sources, including from the instrument itself (“noise”), as well as measured signals that are not the intended observation (“background”). When measurement errors can be quantified and accounted for, measurement accuracy, precision, and uncertainty can all be improved. This often leads to new discoveries in science. This work describes a new technique for quantifying and mitigating measurement error due to backgrounds in the Earth's Van Allen radiation belts. This allows us to measure the inner radiation belt with an increased level of accuracy and precision, enabling new scientific understanding. Specifically, we find that the inner radiation belt is longer lived and of greater intensity than suggested by previous work. Such findings are important scientifically, as they provide ground truth for radiation belt models and allow us to test various theories regarding the growth and decay of the inner radiation belt. This work is also important from a practical standpoint, as it helps improve statistical models that are used for spacecraft design, to determine how best to shield spacecraft and sensitive electronics from the damaging effects of the inner radiation belt. Key Points A new background correction algorithm for relativistic inner zone electrons is developed We find important differences versus the standard algorithm, with several new/clarified features revealed Data from the new algorithm should be used for quantitative inner zone studies at energies >0.7 MeV