In this work, ZrO2 nanocrystals (NCs) are synthesized via a solvothermal treatment in benzyl alcohol, which is an established method for the synthesis of many metal oxide nanocrystals. We found that the use of microwave heating allows for a reduction in reaction time from 2 days in the autoclave to merely 4 h in the microwave. Furthermore, we were able to tune the crystallographic phase from pure cubic to pure monoclinic zirconia by changing the reaction mechanism through the use of a different zirconium precursor. Via GC-MS measurements, we found that the release of a strong acid during synthesis controls the key mechanism behind the control over crystal phase formation. The as-synthesized ZrO2 NCs (cubic or monoclinic) are small in size (3-10 nm), yet aggregated. However, aggregate-free NCs are generated through a surface-functionalization with carboxylic acid ligands, providing stabilization in apolar solvents via steric hindrance. Solution H-1 NMR was used to study the details of this post-modification step and the surface chemistry of the resulting aggregate-free NCs. This led to the conclusion that not only a different crystal structure but also a different surface chemistry is obtained, depending on the precursor composition.