We consider the problem of learning the dynamics in the topology of time-evolving point clouds, the prevalent spatiotemporal model for systems exhibiting collective behavior, such as swarms of insects and birds or particles in physics. In such systems, patterns emerge from (local) interactions among self-propelled entities. While several well-understood governing equations for motion and interaction exist, they are difficult to fit to data due to the often large number of entities and missing correspondences between the observation times, which may also not be equidistant. To evade such confounding factors, we investigate collective behavior from a topological perspective, but instead of summarizing entire observation sequences (as in prior work), we propose learning a latent dynamical model from topological features per time point. The latter is then used to formulate a downstream regression task to predict the parametrization of some a-priori specified governing equation. We implement this idea based on a latent ODE learned from vectorized (static) persistence diagrams and show that this modeling choice is justified by a combination of recent stability results for persistent homology. Various (ablation) experiments not only demonstrate the relevance of each individual model component, but provide compelling empirical evidence that our proposed model - neural persistence dynamics - substantially outperforms the state-of-the-art across a diverse set of parameter regression tasks.