Dimethyl isosorbide (DMI) is a bio-based solvent that can be used as green alternative for conventional dipolar media (dimethyl sulfoxide, dimethylformamide, and dimethylacetamide). The main synthetic procedures to DMI reported in the literature are based on the methylation of isosorbide employing different alkylating agents including toxic halogen compounds such as alkyl halides. A more sustainable alternative would be to employ dimethyl carbonate (DMC), a well-known green reagent and solvent, considered one of the most promising methylating agents for its good biodegradability and low toxicity. Indeed, in recent years, DMC-promoted methylation of isosorbide has been extensively exploited although mostly in the presence of a base or an amphoteric catalyst. In this work, we report for the first time a comprehensive investigation on the synthesis of DMI via DMC chemistry promoted by heterogeneous acid catalyst (Amberlyst-36 and Purolite CT275DR). Reaction conditions were optimized and then applied for the methylation of isosorbide and its epimers, isoidide and isomannide. Considerations on the related reaction mechanism were reported highlighting the difference in the preferred reaction pathways among this new synthetic approach and the previously reported base-catalyzed procedures.