Forecast models of solar radiation incorporating cloud effects are useful tools to evaluate the impact of stochastic behaviour of cloud movement, real-time integration of photovoltaic energy in power grids, skin cancer and eye disease risk minimisation through solar ultraviolet (UV) index prediction and bio-photosynthetic processes through the modelling of solar photosynthetic photon flux density (PPFD). This research has developed deep learning hybrid model (i.e., CNN-LSTM) to factor in role of cloud effects integrating the merits of convolutional neural networks with long short-term memory networks to forecast near real-time (i.e., 5-min) PPFD in a sub-tropical region Queensland, Australia. The prescribed CLSTM model is trained with real-time sky images that depict stochastic cloud movements captured through a total sky imager (TSI-440) utilising advanced sky image segmentation to reveal cloud chromatic features into their statistical values, and to purposely factor in the cloud variation to optimise the CLSTM model. The model, with its competing algorithms (i.e., CNN, LSTM, deep neural network, extreme learning machine and multivariate adaptive regression spline), are trained with 17 distinct cloud cover inputs considering the chromaticity of red, blue, thin, and opaque cloud statistics, supplemented by solar zenith angle (SZA) to predict short-term PPFD. The models developed with cloud inputs yield accurate results, outperforming the SZA-based models while the best testing performance is recorded by the objective method (i.e., CLSTM) tested over a 7-day measurement period. Specifically, CLSTM yields a testing performance with correlation coefficient r = 0.92, root mean square error RMSE = 210.31 μ mol of photons m−2 s−1, mean absolute error MAE = 150.24 μ mol of photons m−2 s−1, including a relative error of RRMSE = 24.92% MAPE = 38.01%, and Nash Sutcliffe’s coefficient ENS = 0.85, and Legate and McCabe’s Index LM = 0.68 using cloud cover in addition to the SZA as an input. The study shows the importance of cloud inclusion in forecasting solar radiation and evaluating the risk with practical implications in monitoring solar energy, greenhouses and high-value agricultural operations affected by stochastic behaviour of clouds. Additional methodological refinements such as retraining the CLSTM model for hourly and seasonal time scales may aid in the promotion of agricultural crop farming and environmental risk evaluation applications such as predicting the solar UV index and direct normal solar irradiance for renewable energy monitoring systems.