Deep learning has already been successfully used in the development of decision support systems in various domains. Therefore, there is an incentive to apply it in other important domains such as agriculture. Fertilizers, electricity, chemicals, human labor, and water are the components of total energy consumption in agriculture. Yield estimates are critical for food security, crop management, irrigation scheduling, and estimating labor requirements for harvesting and storage. Therefore, estimating product yield can reduce energy consumption. Two deep learning models, Long Short-Term Memory and Gated Recurrent Units, have been developed for the analysis of time-series data such as agricultural datasets. In this paper, the capabilities of these models and their extensions, called Bidirectional Long Short-Term Memory and Bidirectional Gated Recurrent Units, to predict end-of-season yields are investigated. The models use historical data, including climate data, irrigation scheduling, and soil water content, to estimate end-of-season yield. The application of this technique was tested for tomato and potato yields at a site in Portugal. The Bidirectional Long Short-Term memory outperformed the Gated Recurrent Units network, the Long Short-Term Memory, and the Bidirectional Gated Recurrent Units network on the validation dataset. The model was able to capture the nonlinear relationship between irrigation amount, climate data, and soil water content and predict yield with an MSE of 0.017 to 0.039. The performance of the Bidirectional Long Short-Term Memory in the test was compared with the most commonly used deep learning method, the Convolutional Neural Network, and machine learning methods including a Multi-Layer Perceptrons model and Random Forest Regression. The Bidirectional Long Short-Term Memory outperformed the other models with an R2 score between 0.97 and 0.99. The results show that analyzing agricultural data with the Long Short-Term Memory model improves the performance of the model in terms of accuracy. The Convolutional Neural Network model achieved the second-best performance. Therefore, the deep learning model has a remarkable ability to predict the yield at the end of the season.