Magnetic tunnel junctions sandwiching a superlattice thin film of iron oxide nanocrystals (NCs) have been investigated. The transport was found to be controlled by Coulomb blockade and single-electron tunneling, already at room temperature. A good correlation was identified to hold between the tunnel magnetoresistance (TMR), the expected magnetic properties of the NC arrays, the charging energies evaluated from current-voltage curves, and the temperature dependence of the junction resistance. Notably, for the first time, a switching from negative to positive TMR was observed across the Verwey transition, with a strong enhancement of TMR at low temperatures.