The use of image based and, recently, deep learning-based systems have provided good results in several applications. Greenhouse trials are key part in the process of developing and testing new herbicides and analyze the response of the species to different products and doses in a controlled way. The assessment of the damage in the plant is daily done in all trials by visual evaluation by experts. This entails time consuming process and lack of repeatability. Greenhouse trials require new digital tools to reduce time consuming process and to endow the experts with more objective and repetitive methods for establishing the damage in the plants.To this end, a novel method is proposed composed by an initial segmentation of the plant species followed by a multibranch convolutional neural network to estimate the damage level. In this way, we overcome the need for costly and unaffordable pixelwise manual segmentation for damage symptoms and we make use of global damage estimation values provided by the experts.The algorithm has been deployed under real greenhouse trials conditions in a pilot study located in BASF in Germany and tested over four species (GLXMA, TRZAW, ECHCG, AMARE). The results show mean average error (MAE) values ranging from 5.20 for AMARE and 8.07 for ECHCG for the estimation of PDCU value, with correlation values (R2) higher than 0.85 in all situations, and up to 0.92 in AMARE. These results surpass the inter-rater variability of human experts demonstrating that the proposed automated method is appropriate for automatically assessing greenhouse damage trials.