Real-world chemical processes often exhibit stochastic dynamics with non-trivial correlations and state-dependent fluctuations. However, most process models simply add stationary noise terms to a deterministic prediction, which can lead to inaccurate predictions. This work proposes using conditional normalizing flows as discrete-time models (DTMs) to learn the stochastic dynamics of chemical processes. Normalizing flows learn an explicit expression of the system states' probability density function (PDF) given prior states and control inputs. The resulting model naturally allows for formulating stochastic and probabilistic setpoint-tracking objectives and chance constraints. In applications to a continuous reactor and a reactor cascade, the normalizing flow yields stable simulations over long time horizons and high-quality results in stochastic and probabilistic MPC formulation for open-loop control. Furthermore, a chance-constrained optimization finds reliable startup controls for the reactor cascade with stochastic reactions. In conclusion, the conditional normalizing flow presents an excellent choice for modeling nonlinear stochastic dynamics.