The productivity of Aspergillus niger cultivations is strongly linked to the pellet morphology. In this article, the agitation‐ and aeration‐induced stress on bio agglomerates is studied. To facilitate investigations, non‐biological particle systems are extensively used to model the actual biological matter. The literature lacks a direct comparison of model systems with the biological system of interest, leaving uncertainties in the applicability of such systems. This work shows that the results for the impellers' stress intensity of three A. niger strains agree qualitatively with the ones of four developed model systems of different nature (s/l, l/l). The findings justify the usage of model systems, despite certain limitations originating from their specific characteristic properties.