Reversible encapsulation allows the direct observation of the isolated molecules under ambient conditions, at equilibrium and in the liquid phase. Here we show that capsules can amplify and stabilize molecules that are present in only trace concentrations in solution. Evidence is given that reversible chemical reactions take place within the capsule. Stabilization of reaction intermediates is a characteristic property of enzymes and is widely regarded as an essential feature of catalytic activity. Reactive molecules can also be stabilized by encapsulation, a process that involves completely surrounding the reactive species within synthetic receptors. Here, we show that self-assembled capsules can isolate and stabilize molecules that are present in only trace amounts in solution. The system amplifies the concentrations of high-energy species with reduced entropies.