Filamentous fungi are widely exploited as cell-factories in industry due to their metabolic diversity, high production capacity and secretion efficiency. In stirred tank bioreactors, the filamentous fungus Aspergillus niger builds agglomerates of complex morphology. The formed morphology has a decisive influence on productivity and is significantly influenced by the hydrodynamic stress induced by the stirrer. Due to the complex interactions between the cultivation parameters, an examination solely of the influence of the stirrer is difficult. In this work, fragmentation experiments were established and conducted allowing the selective examination of the impact of stirrer type and stirring intensity on the bio-agglomerates’ morphology at a reasonable effort. With the applied method, a clear order of stress intensity for different stirrer types was found. Studying the breakage mechanism, both fracture and abrasion have been found to occur, significantly depending on the employed stirrer type. The impeller swept volume model has been proven to correlate the particle size well for the employed stirrer types. In the literature, most work on the characterisation of stirrer types concerning hydrodynamic stress has been done using model systems. The extensive results obtained earlier at our department using a liquid/liquid model system agree with the results of this work.