The encapsulation of guest molecules within polymeric hollow nano- or microscale structures is a rapidly developing field of interdisciplinary research due to a variety of applications ranging from drug delivery and sensor fabrication to nanoscale synthesis and bioinspired mineralization. We report on the encapsulation of pyrene within three-dimensional polypyrrole microvessels synthesized by precipitation polymerization of pyrrole onto toluene droplets that contain pyrene. Steady state and time-resolved fluorescence measurements show that the optical response and dynamics of encapsulated pyrene is significantly different from that in the free solution, likely due to interactions with oligomeric species generated during the polymerization process that partition into the organic core of the microvessel. Our results indicate that the encapsulation process can have a significant influence on the local environment of encapsulated species, an issue that is critical from the perspective of potential synthetic or medical applications.