This paper describes the performance and mechanisms of filtration of biomass with vertical inter-fibre two-phase flow. The effect of bubbling on particle deposition on hollow fibre membranes was studied in a specially designed cross-flow cell in which the fibres were arranged with well-controlled spacing such that slug flow could form between fibres. The enhancement of performance by bubbling and the effect of liquid flow rate, gas how rate, and fibre orientation on filtration performance were investigated. The difference in flux between operation with pump recirculation and airlift systems was also assessed. The results show that bubbling is effective in enhancement of the filtration performance but the enhancement is not sensitive to changes in two-phase flow mixture velocity when the operation is controlled by the deposition in the falling film zone induced by slugs. A theoretical slug-flow mode is developed to illustrate the insensitivity of falling film velocity on mixture velocity. The experiments demonstrate that the axial vertical fibre orientation is superior to transversal orientation for two-phase flow filtration and a higher flux can be achieved with pumped circulation rather than with the airlift system because pumping liquid through the cell can result in a more stable and regular slug flow.