This work examines the effects of polarity on electrospun nanocomposite fibers made of polymer and metal oxide sol solutions. Molybdenum trioxide and Polyvinylpyrrolidone nanocomposites were studied as-spun under straight polarity, i.e., keeping the needle negatively charged and collector grounded and on reverse polarity. The former configuration produced “core-shell” type nanofibers with the polymer encasing the amorphous gel. This was an unexpected result as there was nothing (but electrostatic forces acting on the composite solution within the metallic needle tip) to separate the two materials in such a clear and aligned manner. On studying the effects of reverse polarity on the electrospun nanocomposites, i.e., keeping the needle grounded and the collector negatively charged, the nanofibers morphology was opposite too, by keeping the PVP embedded into the MoO3 matrix, as it was concluded by obtaining a similar diameter wire under as-spun and after a heat treatment to remove the polymer. Parameters such as the relative Zeta potential and electrostatic force appear to play an important role in electrospinning composite nanofibers. Knowing the parameters and their effects will allow tailored processing of biocomposite nanofibers. A model is proposed to explain the findings.