The effect of the AlOx barrier thickness on magnetic and morphological properties of Ta/Co/(AlOx)/Alq3/Si hybrid structures was systematically studied by means of atomic force microscopy, SQUID magnetometry and nuclear magnetic resonance (NMR). All used techniques pointed out that the barrier thickness of 2 nm is required to obtain a magnetically good cobalt layer on top of Alq3. 59Co NMR measurements revealed that the AlOx barrier gives rise to the formation of an interface layer with defective cobalt favouring growth of bulk cobalt with good magnetic properties.