In this work we present a simple and efficient method of nitrogen plasma modification of carbon nanotubes (CNTs). The process allows for treatment of the nanotubes in the form of powder with quite a high yield (65 mg of CNTs per hour). The modified carbon nanotubes contain approx. 3.8% nitrogen, mostly in the pyridinic form. Plasma treated CNTs exhibit better dispersibility in water and higher electric capacitance than pristine CNTs. Modified CNTs are a proper component of novel nanocomposites based on the conducting polymer poly(3,4-ethyleneidoxythiophene). Electrodeposited thin layers of the nanocomposite exhibit improved electrochemical properties (higher capacitance, better stability, lower resistance, faster diffusion) compared to the pure polymer layers.