Sustainable cropping systems based on low inputs have received much attention, even if they may lead to the establishment of a competitive weed flora. This study, conducted from 2011 to 2014 in a Mediterranean environment, evaluated the changes in weed community composition in two cropping systems [conventional (CONV) and organic (ORG)] with different soil tillage [inversion tillage (IT) and non-inversion tillage (NoIT)] in a wheat-tomato-chickpea rotation that began in 2000. The treatments were replicated three times according to a randomised complete block design. The organic system was managed according to EU regulations. Inversion tillage consisted of mouldboard ploughing to a depth of 30cm, while NoIT consisted of subsoiling to a depth of 20cm. Weed control was based on herbicide application in CONV and mechanical weeding in ORG. The organic non-inversion system showed the highest weed biomass (134, 128 and 195gdry matter (DM)m(-2) in wheat, tomato and chickpea, respectively) and weed density (66, 77 and 76plantsm(-2) in wheat, tomato and chickpea, respectively), as well as community richness. However, ORG always increased weed diversity, even if annual dicotyledon species were abundant in ORG-IT and perennial dicotyledon species in ORG-NoIT. The conventional system enhanced the relative frequency of both annual (CONV-IT) and perennial (CONV-NoIT) grasses. There was a negative correlation between density of perennial weeds and crop yield (r(2)=0.24, P<0.001). Therefore, in the Mediterranean environment, combining organic practices with non-inversion tillage could lead to the establishment of perennial weeds that are difficult to control, thus requiring specific weed management practices.