The yield and fruit quality of processing tomatoes (Solanum lycopersicum L.) have increased markedly over the past decades. The aim of this work was to assess the effects of the organic (OFS) and conventional farming systems (CFS) on the main agronomic parameters involved in processing tomato yield components and fruit quality traits of heirloom and modern genotypes. Marketable yield increased from heirloom to modern genotypes, both in OFS and in CFS, showing a difference of ≈20 t per hectare in favor of CFS. Total fruit yield (TY) was not improved from heirloom to modern assessed genotypes, and a difference of ≈35 t per hectare was observed in favor of CFS. In both farming systems, the highest marketable yield of modern genotypes was due to a higher number of fruits per plant, harvest index, nitrogen agronomic efficiency (NAE), and fruit water productivity. Moreover, the main growth parameters involved in the yield differences between OFS and CFS were the number of leaves per plant, the average fruit weight, the normalized difference vegetation index (NDVI), and NAE. It is noteworthy that fruit quality improvement in terms of color and brix per hectare was paralleled by a decrease of tomato pH in both farming systems. According to our results, we conclude that to reduce the current yield gap between OFS and CFS, agronomic and breeding efforts should be undertaken to increase leaf area index, fruit number per plant, and NAE for better genotype adaptation to organic farming systems.