Fungi provide valuable solutions for diverse biotechnological applications, such as enzymes in the food industry, bioactive metabolites for healthcare, and biocontrol organisms in agriculture. Current workflows for identifying new biocontrol fungi often rely on subjective visual observations of strains' performance in microbe-microbe interaction studies, making the process time-consuming and difficult to reproduce. To overcome these challenges, we developed an AI-automated image classification approach using machine learning algorithm based on deep neural network. Our method focuses on analyzing standardized images of 96-well microtiter plates with solid medium for fungal-fungal challenge experiments. We used our model to categorize the outcome of interactions between the plant pathogen Fusarium graminearum and individual isolates from a collection of 38,400 fungal strains. The authors trained multiple deep learning architectures and evaluated their performance. The results strongly support our approach, achieving a peak accuracy of 95.0 % with the DenseNet121 model and a maximum macro-averaged F1-Score of 93.1 across five folds. To the best of our knowledge, this paper introduces the first automated method for classifying fungal-fungal interactions using deep learning, which can easily be adapted for other fungal species.