Magnesium based cement represents one of the most interesting eco-sustainable alternatives to standard cementitious binders. The interest towards this material has a twofold reason: i) its production process, taking place from magnesium silicates, brine or seawater, dramatically reduces the CO2 emissions with respect to those connected with the Portland cement production and ii) it is very well suited to applications for radioactive waste encapsulation. In spite of its potential, the assessment of the structural properties of its binder phase (magnesium silicate hydrate or M-S-H) is far from complete, especially because of its amorphous character. In this work, a comprehensive structural characterization of M-S-H was obtained by means of a multi-technique approach, including a detailed Solid State NMR investigation and, in particular, for the first time, quantitative 29Si Solid State NMR data. M-S-H was prepared through room temperature hydration of highly reactive MgO and silica fume and was monitored for 28 days. The results clearly evidenced the presence in M-S-H of “chrysotile-like“ and “talc-like” sub-nanometric domains, which are approximately in a 1:1 molar ratio for long time hydration. Both these kinds of domains have a high degree of condensation, corresponding to the presence of a small amount of silanols in the tetrahedral sheets. The decisive improvement obtained in the knowledge of the M-S-H structure paves the way for tailoring the macroscopic properties of eco-sustainable cements by means of a bottom-up approach.