The AiiDA workflow manager is an open source tool that allows creating automated workflows for computational science. As such, it employs a strict data provenance tracking, includes an expandable plugin framework and a flexible interface to high performance computing (HPC) resources. AiiDA was primarily developed within the computational material science community. In contrast, the present project explored AiiDA for supporting a workflow in the weather and climate community, more specifically for simulations of atmospheric transport of greenhouse gases and the use of such simulations in estimating greenhouse gas emissions (inverse modelling). Within ExAiRIM, a new AiiDA plugin and graphical user interface (making use of the AiiDAlab platform) was developed for running and post-processing simulations of the atmospheric transport model FLEXPART, in a setup routinely employed in the Atmospheric Modelling and Remote Sensing group at Empa but portable to other FLEXPART users. The plugin allows flexible selection of FLEXPART inputs and the use of various configurations of meteorological inputs that drive the simulations. Furthermore, an interface to Empa's Lagrangian Inversion System (ELRIS) was created, and inversions can now be run through AiiDAlab, based on transport simulations created within AiiDA or imported from elsewhere (e.g., external partners and/or other AiiDA instances). The graphical user interface provides easy access to transport and inverse modelling simulations for non-expert users. Overall, the project achieved the aim of a complete documentation of data provenance and reproducibility of Empa's inverse modelling of national scale greenhouse gas emissions, which we provide annually to BAFU as important information for greenhouse gas mitigation strategies. The tool was presented to other European partners with similar workflows, who are currently investigating the possibility to integrate our approach into their workflows.