Markets for organically produced high quality cotton (Gossypium hirsutum L.) are projected to increase. Field experiments were conducted in Palamas, Karditsa in Central Greece, to compare the effects of two cropping systems on fiber quality of three cotton cultivars. The experiments, conducted during three years, were laid out in a split plot design with four replicates, two main plots (organic and conventional system) and three sub-plots (cotton cultivars). Findings suggest that fiber quality index (FQI), spinning consistency index (SCI) and multiplicative analytic hierarchy process (MAHP) are three indices that could be integrated in a useful protocol for the evaluation of different cropping systems for cotton cultivation. In particular, our results indicate that in general there was not any superiority of conventional compared to the organic cropping system regarding fiber quality as shown by the above mentioned indices. Regarding the length of the cotton fiber, this was positively correlated with micronair and the uniformity index of the cotton fiber. The organic system resulted to higher values of SCI than the ones of the conventional (1547.9 and 1522.3, respectively). The present 3-years study shows that organic cultivation of cotton can ensure high fiber quality and this was clearly confirmed by means of the several important indices.