The texture of pureed fruits and vegetables depends primarily on the original tissue structure and cell wall (CW) properties. However, how variations in the raw fruits’ cellular and molecular structure determine the rheological behaviour of the purees is little understood, though pectin degradation appears to play a key role. Cultivars, fruit load and post-harvest storage were used to obtain raw apples with different tissue structures, which were processed into purees under simulation of an industrial process. The rheological behaviour of the purees was then compared to particle size, pulp wet mass and serum viscosity. The polysaccharide composition of soluble and insoluble CW material were determined after preparation of alcohol insoluble residue. Macromolecular size and molar mass distributions of soluble pectins were analysed using high performance size-exclusion chromatography coupled to multi-angle laser light scattering and online viscometry. Variations in the raw material, especially induced by post-harvest storage, generated a wide range of different puree’s textures. Rheological behaviour of apple purees was driven by particle size, which decreased during prolonged post-harvest storage due to reduced cell adhesion. This was correlated with pectic side chain hydrolysis and modifications in pectin molar mass and structure. Similar trends during storage were observed with different apple cultivars and agricultural practices.