Molecular engineering of manganese(II) diamine diketonate precursors is a key issue for their use in the vapor deposition of manganese oxide materials. Herein, two closely related β‐diketonate diamine MnII adducts with different fluorine contents in the diketonate ligands are examined. The target compounds were synthesized by a simple procedure and, for the first time, thoroughly characterized by a joint experimental–theoretical approach, to understand the influence of the ligand on their structures, electronic properties, thermal behavior, and reactivity. The target compounds are monomeric and exhibit a pseudo‐octahedral coordination of the MnII centers, with differences in their structure and fragmentation processes related to the ligand nature. Both complexes can be readily vaporized without premature side decompositions, a favorable feature for their use as precursors for chemical vapor deposition (CVD) or atomic layer deposition applications. Preliminary CVD experiments at moderate growth temperatures enabled the fabrication of high‐purity, single‐phase Mn3O4 nanosystems with tailored morphology, which hold great promise for various technological applications.