Anomaly detection in high-energy physics is essential for identifying new physics beyond the Standard Model. Autoencoders provide a signal-agnostic approach but are limited by the topology of their latent space. This work explores topology-aware autoencoders, embedding phase-space distributions onto compact manifolds that reflect energy-momentum conservation. We construct autoencoders with spherical ($S^n$), product ($S^2 \otimes S^2$), and projective ($\mathbb{RP}^2$) latent spaces and compare their anomaly detection performance against conventional Euclidean embeddings. Our results show that autoencoders with topological priors significantly improve anomaly separation by preserving the global structure of the data manifold and reducing spurious reconstruction errors. Applying our approach to simulated hadronic top-quark decays, we show that latent spaces with appropriate topological constraints enhance sensitivity and robustness in detecting anomalous events. This study establishes topology-aware autoencoders as a powerful tool for unsupervised searches for new physics in particle-collision data.