Solid electrolytes with extraordinarily high Li-ionic conductivities are key for high performance all-solid-state batteries. So far, the thiophosphate Li10GeP2S12 (LGPS) belongs to the best Li ion conductors with an ionic conductivity exceeding 10 mS cm–1 at ambient. Recent molecular dynamics simulations performed by Dawson and Islam predict that the ionic conductivity of LGPS can be further enhanced by a factor of three if the crystallite size is reduced to the nanometer regime. A change in local ion coordination, hence local disorder, has been assumed to facilitate Li diffusion in the ab-plane of LGPS. As yet, no experimental evidence exists supporting this fascinating prediction. Here, we synthesized nanocrystalline LGPS by high-energy ball milling, characterized the material structurally and probed the Li+ ion transport parameters. Whereas X-ray powder diffraction and high-resolution 31P and 6Li magic angle spinning nuclear magnetic resonance (NMR) spectroscopy helped us to determine morphological changes and local structures upon milling, broadband conductivity spectroscopy in combination with electric modulus measurements allowed us to precisely follow the changes in Li+ ion dynamics. Surprisingly and against the behavior of other electrolytes, ionic conductivity turned out to decrease with increasing milling time, finally leading to a reduction of σ20°C by almost a factor of 10. This decrease affects both, bulk ion dynamics and total conductivity, which also comprises Li+ transport across grain boundary regions in LGPS. As could be shown by NMR, ball-milling leads to a structurally heterogeneous sample with the nm-sized LGPS crystallites being embedded in an amorphous matrix. This amorphous phase is responsible for the reduced performance of the milled electrolyte. Importantly, careful separation of the amorphous and (nano)crystalline contributions to the overall ionic conductivity revealed that even in the nanocrystalline regions Li+ ion dynamics is slowed down compared to untreated, coarse-grained LGPS. We conclude that defects introduced into the LGPS bulk structure via ball milling have a negative impact on ionic transport. We postulate that such kind of structural disorder is detrimental to fast ion transport in materials whose transport properties rely on crystallographically well-defined diffusion pathways.