The ever-growing market of protein-based therapeutics as well as the advent of biodegradable and non-toxic polymers has boosted research in the field of protein encapsulation using nano- and microparticles. Although such small carriers are promising tools for protein administration, hurdles still exist, making protein formulation a difficult task. This review discusses the scientific issues that should be taken into account when encapsulating therapeutic protein drugs into biodegradable polymeric nano- and microparticles. It mostly deals with the manufacturing procedures of the particles and with the analysis of the encapsulated proteins. Sample preparation prior to qualitative or quantitative analysis is discussed together with the analytical methods employed. Indeed, the entrapped protein can be correctly analyzed only if the sample preparation and drug analysis minimize drug loss and degradation. The most common encountered pitfalls are reviewed and commented upon to emphasize specific concerns, which require closer scrutiny.