Tomato is a very important vegetable crop in Italy. Improving the means of production for processing organic tomatoes could help guarantee better profits for farmers and, at the same time, enhance environmental management and safeguard consumers’ health. Weed control, in particular within crop rows, is one of the main problems in organic farming, and thus also for the organic cultivation of tomato. The aim of this study was to develop innovative strategies and equipment for effective physical weed control in processing tomatoes. A conventional weed management system incorporating herbicides was compared with an alternative system relying exclusively on physical control during three growing seasons (2006–2008) on a farm located near Pisa, Italy. The crop was transplanted mechanically onto paired rows. The conventional strategy consisted of three different chemical treatments, two post-transplanting PTO-powered rotary hoe passes and several hand-weeding treatments on the paired rows. The alternative system included a stale seedbed technique (performed by a rolling harrow pass and one flaming treatment), two post-transplanting precision hoeing treatments and several hand-weeding treatments. All the machines for the alternative system were adjusted and set up for processing tomatoes transplanted in paired rows. Each physical treatment (mechanical and thermal) within the alternative system allowed an ‘instantaneous’ (just before/just after) weed control from 50 to 100%, while the alternative strategy as a whole achieved values of weed dry biomass at harvest ranging from 22 to 126 g m−2. However, the alternative system required a total labor input that averaged 50% higher than the conventional strategy. The conventional system had on average more effective weed control than the alternative system, but both strategies controlled weeds effectively. Weed biomass at harvest averaged 36 and 68 g m−2 for conventional and alternative strategies, respectively. On the other hand, the alternative system generally led to a significant increase in fresh crop yield (+13% average yield for the 3 years).