Immobilization and display of proteins is extensively used to enhance stability and performance of proteins for technical uses such as in biotechnology. Here, self‐assembled nonporous polyhydroxybutyrate (PHB) particles bioengineered to display proteins of interest are subjected to alginate encapsulation processes. The novel composite spheres are fabricated using ionotropic gelation methods. The immunoglobulin G (IgG) binding domain Z and organophosphate hydrolase (OpdA) are attached to PHB particles, and are examples for bioseparation and bioremediation applications, respectively. Alginate microspheres entrapping Z domain coated PHB particles enable flow‐through purification of IgG. Microsphere porosity is pH tunable and at acidic pH IgG is released from Z domains but retained within microspheres. OpdA‐PHB particles are functionally entrapped in alginate microspheres enabling flow‐through substrate conversion. Attachment of functional proteins to PHB particles enhances retention within the alginate microspheres. The hydrophobic PHB particle core within alginate beads provides payload for lipophilic substances, which adsorption kinetics are aligned with a pseudo‐second‐order kinetic model in agreement with the Freundlich isotherm model. This study describes the development of a multifunctional composite material platform based on alginate spheres encapsulating PHB particles that provide payload for lipophilic substances and can be engineered to display protein functions of interest.