Conditional Normalizing Flows (CNFs) are flexible generative models capable of representing complicated distributions with high dimensionality and large interdimensional correlations, making them appealing for structured output learning. Their effectiveness in modelling multivariates spatio-temporal structured data has yet to be completely investigated. We propose MotionFlow as a novel normalizing flows approach that autoregressively conditions the output distributions on the spatio-temporal input features. It combines deterministic and stochastic representations with CNFs to create a probabilistic neural generative approach that can model the variability seen in high-dimensional structured spatio-temporal data. We specifically propose to use conditional priors to factorize the latent space for the time dependent modeling. We also exploit the use of masked convolutions as autoregressive conditionals in CNFs. As a result, our method is able to define arbitrarily expressive output probability distributions under temporal dynamics in multivariate prediction tasks. We apply our method to different tasks, including trajectory prediction, motion prediction, time series forecasting, and binary segmentation, and demonstrate that our model is able to leverage normalizing flows to learn complicated time dependent conditional distributions.