Charge ordering (Fe+3/Fe+2) is a key concept in the Verwey transition of Fe3O4 because it frequently competes with functional properties (half-metallicity/ferromagnetism and structural transformation) and quantum confinement effect, especially at nanoscale dimensions. In this paper, we report the fabrication of nanocrystalline Fe3O4 thin films via two different reduction routes, namely, vacuum annealing and wet H2 annealing. While vacuum annealed films exhibit Verwey transition and resistivity values comparable to bulk Fe3O4, the same is not observed in electric transport properties of wet H2 annealed films. However, this transition was visible in the magnetic characteristics exhibited by both the films though realized via different routes. This observation indicates the possibility of charge and spin ordering as two independent phenomena, and it is a coincidence that happens at the same Verwey transition region. It is seen that a crossover from thermally activated hopping (300–120 K) to Mott variable range hopping (VRH) (across Verwey transition) and then to Shklovskii–Efros VRH hopping (70–30 K) via the conduction mechanism takes place in vacuum annealed films in contrast to the typical semiconducting behavior (300–50 K) expected of wet H2 annealed films. Different electric transport properties in both varieties of Fe3O4 films could be ascribed to the electronic disorder/defects affecting charge ordering Fe+3/Fe+2 and trimerons (Fe+3–Fe+2–Fe+3).