Indoor hydroponic greenhouses are becoming increasingly popular for sustainable food production. On the other hand, precise control of the climate conditions inside these greenhouses is crucial for the success of the crops. Time series deep learning models are adequate for climate predictions in indoor hydroponic greenhouses, but a comparative analysis of these models at different time intervals is needed. This study evaluated the performance of three commonly used deep learning models for climate prediction in an indoor hydroponic greenhouse: Deep Neural Network, Long–Short Term Memory (LSTM), and 1D Convolutional Neural Network. The performance of these models was compared at four time intervals (1, 5, 10, and 15 min) using a dataset collected over a week at one-minute intervals. The experimental results showed that all three models perform well in predicting the temperature, humidity, and CO2concentration in a greenhouse. The performance of the models varied at different time intervals, with the LSTM model outperforming the other models at shorter time intervals. Increasing the time interval from 1 to 15 min adversely affected the performance of the models. This study provides insights into the effectiveness of time series deep learning models for climate predictions in indoor hydroponic greenhouses. The results highlight the importance of choosing the appropriate time interval for accurate predictions. These findings can guide the design of intelligent control systems for indoor hydroponic greenhouses and contribute to the advancement of sustainable food production.