To mimic organelles and cells and to construct next-generation therapeutics, asymmetric functionalization and location of proteins for artificial vesicles is thoroughly needed to emphasize the complex interplay of biological units and systems through spatially separated and spatiotemporal controlled actions, release, and communications. For the challenge of vesicle (= polymersome) construction, the membrane permeability and the location of the cargo are important key characteristics that determine their potential applications. Herein, an in situ and post loading process of avidin in pH-responsive and photo-cross-linked polymersomes is developed and characterized. First, loading efficiency, main location (inside, lumen, outside), and release of avidin under different conditions have been validated, including the pH-stable presence of avidin in polymersomes’ membrane outside and inside. This advantageous approach allows us to selectively functionalize the outer and inner membranes as well as the lumen with several bio(macro)molecules, generally suited for the construction of asymmetrically functionalized artificial organelles. In addition, a fluorescence resonance energy transfer (FRET) effect was used to study the permeability or uptake of the polymersome membrane against a broad range of biotinylated (macro)molecules (different typology, sizes, and shapes) under different conditions.