This work presents a facile reactive template route to prepare polypyrrole (PPy) with a given, chosen nanostructure among three different morphologies (i.e., nanotubes, nanofibers and urchins). This approach exploits the variability of MnO2 morphologies and its versatility as sacrificial template. The morphological evolution for this template-assisted growth of PPy nanostructures has been briefly explained. These unique architectures significantly enhance the electroactive surface area of the PPy nanostructures, leading to better interfacial/chemical distribution at the nanoscale, fast ion and electron transfer and good strain accommodation. Thus, when used as supercapacitor electrodes, a maximum specific capacitance of 604 F/g at a current density of 1.81 A/g was reached for PPy nanofibers. Even after more than 1000 cycles at 9 A/g, a capacitance of 259 F/g with 91% retention was achieved. Moreover, the same PPy nanofibers can be used as cathode material for lithium-ion batteries (LIBs), showing a capacity of 70.82 mAh/g at a rate of 0.10 C with good cycling stability and rate capability. Our results provide sound evidences that PPy nanostructures can be properly tuned and make the difference for the practical application of these materials in electrochemical energy storage devices.