The production of agricultural products and the high yield in these products are of critical importance for the continuation of human life. In recent years, machine learning and deep learning technologies have been widely used in determining agricultural productivity. The purpose of this study was to estimate the yield of apple fruit by using a novel deep learning-based hybrid method. First, by using images belonging to the golden and royal gala apple varieties, a classification was made with the help of a convolutional neural network (CNN) that was designed for the study. Then, using classical machine learning algorithms and bagging and boosting algorithms, a hybrid application was performed by classifying the images whose feature extractions were done with the designed CNN. The results of the study, presented on 4 separate datasets (Datasets A, B, C, and D), were evaluated based on accuracy, precision, recall, F-measure, and Cohen kappa scores. Considering the accuracy results for Datasets B, C, and D, it was determined that the hybrid model that gave the best result was the CNN-SVM model. For Dataset A, the CNN-SVM and CNN-Gradient Boosting hybrid models gave the best and same accuracy. Dataset C was determined as the most appropriate dataset in terms of the more balanced distribution of train, test, and validation size in the datasets, the results of the proposed hybrid CNN model, and the evaluation of the results of the model. For Dataset C, it was found that the accuracy of the hybrid model was 99.70%. Precision, recall, f-measure, and Cohen kappa scores were 99%. The results of the study revealed that the hybrid models showed effective results in determining the productivity of apple fruit through images belonging to the golden and royal gala varieties.INDEX TERMS Apple yield prediction, deep learning, ensemble methods, machine learning, smart farm.