Dealing with non-stationarity in environments (i.e., transition dynamics) and objectives (i.e., reward functions) is a challenging problem that is crucial in real-world applications of reinforcement learning (RL). Most existing approaches only focus on families of stationary MDPs, in which the non-stationarity is episodic, i.e., the change is only possible across episodes. The few works that do consider non-stationarity without a specific boundary, i.e., also allow for changes within an episode, model the changes monolithically in a single shared embedding vector. In this paper, we propose Factored Adaptation for Non-Stationary RL (FANS-RL), a factored adaption approach that explicitly learns the individual latent change factors affecting the transition dynamics and reward functions. FANS-RL learns jointly the structure of a factored MDP and a factored representation of the time-varying change factors, as well as the specific state components that they affect, via a factored non-stationary variational autoencoder. Through this general framework, we can consider general non-stationary scenarios with different changing function types and changing frequency. Experimental results demonstrate that FANS-RL outperforms existing approaches in terms of rewards, compactness of the latent state representation and robustness to varying degrees of non-stationarity.