The hyperspectral EnMAP (Environmental Mapping and Analysis Program) satellite was successfully launched in April 2022, passed its commissioning phase, and entered the nominal phase of operational data acquisition in November 2022. Since then, users may submit data acquisition proposals and download the data in three processing levels: Level-1B (radiometrically-corrected and spectrally-characterized top-of-atmosphere (TOA) radiance), Level-1C (geometrically-corrected L1B data), and Level-2A (atmospherically-corrected Level-1C data, i.e., bottom-of-atmosphere (BOA) reflectance). The official product generation is usually done by the ground segment processing chain. Alternatively, the EnMAP processing tool (EnPT) provides a highly customizable free and open-source pre-processing chain enabling additional functionalities and options to fulfill individual user requirements and quality expectations. Here, we provide an overview of the implemented pre-processing chain and its modular design with a specific focus on the additional functionalities of EnPT to obtain highly accurate and customizable hyperspectral EnMAP Level-2A data.