Chromium oxides with the spinel structure have been predicted to be promising high voltage cathode materials in magnesium batteries. Perennial challenges involving the mobility of Mg2+ and reaction kinetics can be circumvented by nano-sizing the materials in order to reduce diffusion distances, and by using elevated temperatures to overcome activation energy barriers. Herein, ordered 7 nm crystals of spinel-type MgCr2O4 were synthesized by a conventional batch hydrothermal method. In comparison, the relatively underexplored Continuous Hydrothermal Flow Synthesis (CHFS) method was used to make highly defective sub-5 nm MgCr2O4 crystals. When these materials were made into electrodes, they were shown to possess markedly different electrochemical behavior in a Mg2+ ionic liquid electrolyte, at moderate temperature (110 °C). The anodic activity of the ordered nanocrystals was attributed to surface reactions, most likely involving the electrolyte. In contrast, evidence was gathered regarding the reversible bulk deintercalation of Mg2+ from the nanocrystals made by CHFS. This work highlights the impact on electrochemical behavior of a precise control of size and crystal structure of MgCr2O4. It advances the understanding and design of new cathode materials for Mg-based batteries.