Calcium silicate hydrate (C-S-H) is the main binding product of ordinary Portland concrete (OPC). Unfortunately, OPC production generates ∼5% of all anthropomorphic CO2. Among the most promising green alternatives, magnesium silicate hydrate (M-S-H) is a colloidal gel equivalent to C-S-H which exhibits weaker mechanical properties. Here we investigated the effect of the inclusion of aluminosilicate nanoclays (HNTs) on the microstructure of the silicate hydrate gels as a strategy to ultimately improve their mechanical properties. The microstructure of C-S-H and M-S-H gels synthesized with and without carboxylic or polycarboxylic functionalised HNTs (HNT-COOH, HNT-PAA) was investigated by a multi-technique approach including small- and wide-angle X-ray scattering (SWAXS) and scanning electron microscopy (SEM). The results indicate that, during C-S-H formation in solution, HNTs decrease the size of the disk-like globules with little influence on the spacing of calcium silicate layers. In the case of M-S-H, the presence of functionalised HNTs has a reduced effect on the hydrate structure as a result of the weaker interaction of the carboxylic moieties with Mg2+ ions. SEM investigation on the synthesized composites shows that HNT-PAA are better included in the hydration products. Moreover, in the proximity of the PAA functionalised surfaces, less extended aggregates are formed. The morphology at the micron scale for M-S-H and C-S-H with HNT-COOH is conserved.