The paper deals with the effect of various modifications of composition and homogenization procedure on micromechanical characteristics of high-performance concrete (HPC) containing supplementary cementitious materials (SCMs), namely silica fume, fly ash and metakaolin. The main motivation was to characterize the changes of microstructure induced by the type and amount of SCMs, by the time and order of mixing of components and by coarse aggregate washing. The effects of the changes of microstructure on macroscopic mechanical features of the material were also studied. Indentation moduli of particular phases of the material were measured by nanoindentation. Interfacial transition zone (ITZ) thickness was primarily measured by nanoindentation. An alternative method of ITZ thickness determination based on variations in chemical composition was tested for a selected sample with encouraging result. Compressive strength and bulk elastic modulus of concrete were determined by standard loading tests. The results showed that SCMs generally decrease the thickness of ITZ, but no direct relation to compressive strength of concrete was found for mixtures with variable SCMs content. In case of mixtures with optimized SCMs content prepared by different homogenization procedures or with the use of aggregate washing, qualitative dependence between ITZ thickness and compressive strength was found. Aggregate washing proved to be useful for improving both microscopic and macroscopic properties, having positive effect on ITZ thickness, compressive strength, bulk elastic modulus and indentation moduli of particular phases.