•Chitosan microbeads were prepared by emulsion crosslinking technique.•Thyme polyphenols were encapsulated by simultaneous swelling/encapsulation processes.•The behavior of microbeads was examined in simulated gastrointestinal conditions.•The high loading degree and significant antioxidant potential were achieved.•The obtained encapsulation system can be used as a functional food additive. In this work chitosan microbeads were prepared by emulsion technique and loaded with thyme polyphenols by diffusion from an external aqueous solution of Thymus serpyllum L. The effects of concentrations of chitosan (1.5–3% (w/v)) and GA (glutaraldehyde) (0.1–0.4% (v/v)), as a crosslinking agent on the main properties of microbeads were assessed. The obtained microgel beads from ∼220 to ∼790μm in diameter were exposed to controlled drying process at air (at 37°C) after which they contracted to irregular shapes (∼70–230μm). The loading of dried microbeads with polyphenols was achieved by swelling in the acidic medium. The swelling rate of microbeads decreased with the increase in GA concentration. Upon this rehydration, thyme polyphenols were effectively encapsulated (active load of 66–114mgGAEgbeads−1) and the microbeads recovered a spherical shape. Both, the increase in the amount of the crosslinking agent and the presence of polyphenols, contributed to a more pronounced surface roughness of microbeads. The release of encapsulated polyphenols in simulated gastrointestinal fluids was prolonged to 3h.