Granular flow processes involving different interstitial fluids and coupling regimes are widespread in both natural systems (e.g., landslides, rock avalanches, river sediment transport) and industrial applications (e.g., aggregates in concrete manufacturing, powder technology, animal feed). Despite this, the behaviour of complex granular flows is not fully understood. Modelling of granular media through software packages that couple the Discrete Element Method with Computational Fluid Dynamics (DEM-CFD) enables a comprehensive description of granular small-scale mechanics through simulations of particle-particle and particle-fluid interactions at high temporal and spatial resolution. These approaches are pivotal in the development of constitutive models that represent the bulk rheology of granular media. While DEM-CFD simulations provide particle-scale information (e.g., particle velocities and forces), extracting continuum fields requires a discrete-to-continuum (D2C) transformation that applies a mathematical approach termed coarse-graining. Although some DEM software packages include built-in D2C capabilities, others, such as MFiX-DEM, do not. Consequently, users are often required to develop custom D2C workflows or adapt simulation outputs to the requirements of other D2C tools. Hence, we introduce Pysammos, a Python package that performs discrete-to-continuum transformations and is designed to be user-friendly, open-source, and computationally efficient. Pysammos is able to process polydisperse granular mixtures of any particle shape, while also offering the option to analyse different particle phases separately. It post-processes output files from MFiX-DEM software and produces vtkhdf outputs ready for visualisation in ParaView, as well as a more generic h5 format for further data analysis. Pysammos is able to operate on standard desktop computers as well as on HPC systems. Finally, we showcase a variety of exemplar applications such as sediment erosion, crystals and magma in a conduit, bedload transport and impact cratering.