The lotus seed and lily bulb beverage (LLB) has a problem with solid particle sedimentation. To address this issue, LLB was homogenised twice at different pressures (0~100 MPa) using a homogeniser. This study aims to investigate the changes in the particle size distribution (PSD), microstructure, rheological behaviour, sedimentation index (IS), turbidity, physicochemical properties, and sensory quality of LLBs after homogenisation treatments. The results regarding PSD and microstructure showed that the suspended particles were decomposed at high pressure with increasing homogenisation pressure, forming small particles of cellular material, cell wall fragments, fibre fractions, and polymers. The LLB showed shear-thinning behaviour and weak gelation characteristics (G′ > G″) and rheological properties. Among all homogenisation pressures, the 60 MPa sample showed the lowest sedimentation rate and the highest turbidity. When the pressure was increased from 0 to 100 MPa, the total soluble solid (TSS) content showed an upward trend, while the ascorbic acid content (AAC) gradually decreased. The highest sensory evaluation was observed in the 60 MPa sample in terms of overall acceptability.