Within the framework of a European project, Agroscope set up a trial regarding organic vegetable cultivation in greenhouses in Conthey, Switzerland. The aim of the trial was to develop an even more sustainable cultivation method than usual organic farming. Therefore, diversity in crop rotation and biodiversity were increased and soil-damaging treatments, as copper and sulfur applications, together with inputs of commercial organic fertilizers were avoided. A comparison of two usual organic systems called BAU1 and BAU2 (Business As Usual) with two innovative systems called INN1 and INN2 was carried out in Venlo type greenhouse from November 2018 to November 2020. In order to verify the efficiency of the tested innovative systems, tomato yield and quality were analyzed, as well as the soil microbiological activity throughout the trial duration. Tomato quality and yields were found to be the highest in the usual organic production system BAU1 with the highest energy inputs for heating. However, it is interesting to note that the yields of the innovative systems INN1 and INN2 were equivalent to that of the usual organic system BAU2 under similar reduced heating procedure. This shows that fertilizer types such as mulch and green manure, which contribute also to soil quality, are an interesting alternative to commercial organic fertilizers. Finally, the analyses of soil microbiological activity showed that the INN1 and INN2 system stands out from the BAU2 system in 2020, especially in May and July.