High-energy milling (HEM) was used to produce nixtamalized corn flours, the traditional nixtamalization process was used as a control. Four creole grains were stone-milled, adjusted to an appropriate moisture content and calcium hydroxide concentration and milled using HEM. The physicochemical, thermal, and rheological characteristics of the flours and corn masas were affected by the HEM process. Negritas and Ahualulco creole grains nixtamalized by HEM showed similar viscosity profiles as a control. HEM reduced the gelatinization enthalpy compared to control and raw flours. Diffractograms showed changes in the crystalline structures and FT-IR demonstrated different regions for lipids, proteins, and carbohydrates in all control and treated grains. The texture of corn masas revealed significant differences according to the grain type. ESEM analysis showed smaller particles of HEM flours compared to those of the control. HEM could be a faster, non-pollutant, energy-saving, alternative nixtamalization process.