In this research study, we investigated the morphology of polypyrrole nanostructures, which were formed during the electrochemical deposition of conducting polymer. An electrochemical quartz crystal microbalance (EQCM) cell equipped with a flow-through system was employed to exchange solutions of different compositions within the EQCM cell. When bare PBS buffer in the EQCM cell was exchanged with PBS buffer with pyrrole we observed a distinct increase in the resonance frequency Δf. This change in the resonance frequency and electrical capacitance, which was calculated from electrochemical impedance spectroscopy (EIS) data, illustrate that pyrrole on the surface of the gold electrode formed an adsorbed layer (adlayer). The formation of a pyrrole adlayer before the potential pulse that induced polymerization was investigated by QCM-based measurements. The electrochemical polymerization of this adlayer was induced by a single potential pulse and a nanostructured layer, which consisted of adsorbed polypyrrole (Ppy) nanoparticles with a diameter of 50 nm, was formed. QCM and EIS data revealed that by the next cycle of the electrochemical formation of Ppy, which was investigated after flow-through-based exchange of solutions, the initially formed Ppy surface was covered by the adlayer of pyrrole. This adlayer was desorbed when pyrrole was removed from the solution. When electrochemical polymerization was performed using 50 potential pulses, a Ppy layer, which had more complex morphology, was formed on the EQCM crystal. Scanning electron microscopy showed that the conductivity of this layer was unequally distributed. We observed that the polypyrrole layer formed by electrochemical deposition, which was performed using potential pulses, was formed out of aggregated spherical Ppy particles with a diameter of 50 nm.