Abstract The effects on the sensory perception of texture, rheology and microstructure of processed cheese analogue made with different milk protein bases, and substitution of milk fat by starch or microparticulate whey protein were studied. Differences in rheological properties of the products were influenced by (a) the duration of storage, (b) the cohesiveness character with respect to the lipid content, and (c) the compression response and spreadability characteristics with respect to lipid, storage period and/or base; the latter two aspects peaked at 2 months and then dropped to their initial values. Scanning and transmission electron microscopy revealed differences in the microstructure of processed cheese analogues. Products made with anhydrous milk fat contained higher concentrations of fat globules compared with analogues made with fat-substitutes. Electron-dense particles were evident in all the products, which could be undissolved protein aggregates or fat-substitutes, and no correlations could be found between such images and the rheological properties of processed cheese analogues. The porosity of the protein matrix was denser in processed cheese analogues made with high-protein skimmed milk powder.