Microalgae biomass is seen as a sustainable and socially more responsible feedstock for the production of biofuels and other fine chemical products. Dewatering algae using membrane filtration is a leading technology, however the associated costs are typically not determined. This work investigates the filtration of Chlorella minutissima using a pilot-scale cross-flow microfiltration unit. A filtration model was developed and validated based on permeate flux as a function of biomass concentration (0.6–19.0 dry cell weight/L) and transmembrane pressure (ΔP, 1.80–2.10bar). Processing times for harvesting C. minutissima were determined by iteration of the model and costs were related to energy consumption. For the experimental conditions of 1.95bar, 1.0gDCW/L initial biomass concentration, 0.70kWh, 25°C and 3.8m2 membrane area, harvesting costs were determined as 2.86kWh/kg biomass. Subsequent investigation of the influence of the operating parameters and scale-up effects demonstrated that significant cost reduction to 1.27kWh/kg biomass was possible at 1.95bar, 2.0gDCW/L initial biomass concentration, 0.46kWh, 20°C and 7.6m2 membrane area. Further, biomass concentration was demonstrated to be one of the major drivers to reduce the cost of harvesting microalgae. Membrane filtration was demonstrated to be a feasible harvesting process allowing biomass concentrations up to 150gDCW/L without using chemicals which complicate the downstream processing stages.