The food industry has shown an increased interest in the manufacture of healthier and more natural food products. By tailored processing fruit and vegetables can be used as structurants thus reducing artificial gums and stabilisers. The effect of different thermal and mechanical treatments, including high-pressure homogenisation, on the microstructural and rheological properties of carrot, broccoli and tomato dispersions was studied. As part of the rheological characterisation small oscillatory deformation as well as shear flow measurements were performed. Carrot and broccoli showed a different behaviour from tomato under the conditions studied. Changing the order of thermal and mechanical treatment led to microstructures with different flow properties. The resulting microstructures differed in the manner of cell wall separation: either breaking across the cell walls or through the middle lamella. High-pressure homogenisation decreased the viscosity of carrot and broccoli dispersions, while it increased the viscosity of tomato. Cryo-scanning electron microscopy showed that the cell walls of carrot and broccoli remained as compact structures after homogenisation whereas tomato cell walls were considerably swollen. Based on the type of vegetable, the different processes applied led to microstructures with different rheological properties. This study shows that particle size distribution, morphology and phase volume are important parameters to explain the complex relationship between rheology and microstructure for these types of systems.