Grey mould caused by Botrytis cinerea is an endemic disease in greenhouse tomato crops in the Mediterranean Basin, where the scarcity of heating systems together with the winter weather conditions makes the use of fungicides necessary. The availability of fungicides for organic tomato production is limited, and traditionally, farmers have used copper-based formulations. In the present work, in vitro tests with twelve commercial formulations resulted in cinnamon extract and potassium hydrogen carbonate (PHC) showing high efficacy in the inhibition of B. cinerea growth. Both formulations were evaluated in on-farm greenhouse trials conducted for two seasons (2019/2020 and 2020/2021) in three greenhouses located in Almería, Spain. In terms of controlling Botrytis, PHC showed efficacy results comparable to or even better than those that have been obtained for copper oxychloride. Weather conditions outside and inside the greenhouse were conducive to the onset and development of the disease. Tomato variety selection and pruning practices (flush cuttings) were the main factors that reduced the use of copper-based formulations or any other fungicide to prevent grey mould infection. Smart and integrated management of the mentioned factors could lead to the substitution of copper to control Botrytis in the crop system studied here.