Animal models of neurodegenerative diseases are useful tools to investigate neurodegenerative diseases. However, there is often a wide variety of described models for a same pathology, each model exhibiting its own characteristics. In this work, we used two mouse models of Huntington’s disease exhibiting very different alterations. Using a protocol combining gluCEST imaging and 1H-MRS, we showed that, while gluCEST may evidence alterations in unexpected brain regions, it may also be blind to disease process in certain situations where glutamate levels are preserved. This highlights the complementarity of both methods to identify relevant biomarkers of the pathology.