This work introduces a novel method to generate probabilistic hub‐height wind speed forecasts aimed at power output prediction. We employ state‐of‐the‐art convolutional variational autoencoders (CVAEs) trained with historical wind speed observations, multivariable outputs (wind speed, direction, temperature, pressure, and humidity) from a numerical weather prediction (NWP) model and spatio‐temporal encodings. After training, we exploit the CVAE data generating capabilities to produce probabilistic forecasts from the same deterministic dynamical NWP model. The resulting probabilistic forecast provides an insight into the uncertainty of the original deterministic input that compensate for errors due to numerical discretization, inaccuracies in initial/boundary conditions and parameterizations and, most importantly wind speed fluctuations due to complex terrain features. To show the performance of the proposed model, we validate the approach with forecasted and observed data for fifteen sites in a wind farm in Awaji Island, Japan, in a challenging zone with complex topography and highly fluctuating wind patterns. We show that the proposed method provides improved wind speed forecasts from both deterministic (reduced root mean square error) and probabilistic (reduced continuous ranked probability score) standpoints. We also use ensemble forecast validation methods to assess the statistical properties of the CVAE and conclude that in zones with rapidly changing wind speed dynamics, the CVAE ensemble performs in a superior way when compared to the analog ensemble method. Finally, we also provide an insight on how the results can be used to obtain reliable wind power estimations.