This research aimed to understand and describe the effect of the molecular structure of Polycarboxylate ether superplasticisers (PCE) on the thixotropic structural build-up and the viscosity of low clinker concretes (LCC). We investigated non-commercial PCE superplasticisers with varying side chain lengths, densities, and backbone lengths. Thixotropic structural build-up and viscosity were determined in an application-oriented approach of constant workability, i.e. slump flow, adjusted by the PCE dosage. The investigations were carried out on paste, mortar, and concrete scale. Additionally, colloidal particle interactions, hydration kinetics, and the particle microstructure were quantified. The key colloidal and contact interactions modified by the PCE were identified to bridge the gap between effects at the nano-scale (PCE molecular parameters, colloidal interactions, hydration) and the macro-scale (rheological properties, particularly viscosity and thixotropic structural build-up). The objective was to gain a comprehensive understanding of the effects of PCE molecular structure on thixotropy and viscosity in low clinker binder systems with high SCM contents, to control the fresh properties of concrete, and to enable predictions crucial for future applications of LCC.