The use of microfiltration as an alternative to pasteurisation to reduce the microbial load of raw skimmed milk is a well established technology. However, its application in reducing bacteria from highly viscous dairy based solutions has not due to issues of low flux and high fouling tendency. This study involves the application of microfiltration to remove spores from high solids content Milk Protein Isolate (MPI) solutions. MPI feeds were inoculated with Bacillus mycoides spores a safer alternative to Bacillus cereus, a psychrotrophic spore forming bacteria found in dairy feeds. Suitable protocols for MPI resolubilisation, Bacillus mycoides cell and spore preparations were established and the membranes, MPI and spores were fully characterised by scanning electron microscopy (SEM), particle size distribution, rheology and pure water flux (PWF) measurements. Feed and permeate samples collected during experiments were analysed for solids content by oven drying, protein content using the Bradford assay and spore content using PetrifilmTM Aerobic count plates. To try and determine an optimum protocol for MPI filtration, a variety of filtration rig set-ups, modules and membranes were tested. Experiments were carried out at different MPI concentrations (4 – 16 wt%), cross flow velocities (CFV’s) (0.7 – 2.0 m s-1) and transmembrane pressures (TMP’s ) (1 and 2 bar). The filtration of 15 wt% MPI proved challenging. The best set of results were obtained using the 12.0 μm membrane at 1.4 m s-1, producing a 27 LMH flux, 96.5% protein transmission and a 2.1 log spore reduction. These results indicate that large pore ceramic microfiltration may be a suitable technology to replace or augment pasteurisation for high solids content dairy feeds. The effect of backwashing using different durations and frequencies was investigated. Backwashing parameters of 10 seconds every 5 minutes at 1 bar were found to be the most effective. The optimum cleaning regime found for MPI fouled ceramic membranes involved a long rinsing backflush at 1 bar, acid and alkali steps without backwashing, which produced a 99.6% flux recovery.