pynxtools is a Python package that provides core functionalities for converting experimental data into HDF5 files that are compliant with NeXus application definitions (https://manual.nexusformat.org/classes/applications/index.html). During the data conversion process it performs data verification (e.g., checking for expected data types) to ensure compliance with the chosen NeXus application definition. In addition to its standalone capabilities, pynxtools offers an interface for developing custom reader plugins to convert experimental raw data into structured HDF5 formats. The package can also be used as a plugin for the NOMAD platform (https://nomad-lab.eu/nomad-lab/), a distributed web-based system for managing materials science data, allowing users to convert experimental data directly into the NOMAD metainfo format. The resulting HDF5 files are parsed and stored in the NOMAD central database, ensuring that the data remains findable, accessible, interoperable, and reusable (FAIR). This work is part of the FAIRmat project (project ID 460197019), funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) (https://gepris.dfg.de/gepris/projekt/460197019?language=en). Visit the [FAIRmat page](https://www.fairmat-nfdi.eu/fairmat/about-fairmat/consortium-fairmat) for more info.