Nature uses bottom-up approaches for the controlled assembly of highly-ordered hierarchical structures with defined functionality, such as organelles, molecular motors and transmembrane pumps. The field of bionanotech-nology draws inspiration from nature by utilizing biomolecular building blocks such as DNA, proteins and lipids, for the (self-) assembly of new structures, devices and systems for applications in biomedicine, optics or electronics. Amongst the toolbox of available building blocks, proteins that form cage-like structures, such as viruses and virus-like particles, have been of particular interest since they can be readily modified genetically or chemically both on the outer or inner surface, and form highly symmetrical assemblies. Bacterial encapsulins are a class of non-viral protein cages that self assemble into stable icosahedral structures. Using teal fluorescent proteins (TFP) engineered with a specific native C-terminal docking sequence, we report the molecular self-sorting and selective packaging of TFP cargo into bacterial encapsulins during in vivo assembly. Using native mass spectrometry techniques, we show that loading of either monomeric or dimeric TFP cargo occurs with unprecedented high fidelity and exceptional loading accuracy. Such self-assembling systems equipped with self-sorting capabilities would open up a new realm of exciting opportunities in nanotechnology, for example, as artificial (molecular storage or detoxification) organelles or as artificial cell factories for in situ biocatalysis.