Background: Bursera microphylla (B) A. Gray, a plant native to northwest Mexico, has long been utilized in traditional medicine for its anti-inflammatory effects. Previous studies have highlighted the bioactivity of B. microphylla fruit extract. Chitosan (Cs), a biopolymer known for its favorable physicochemical properties, has proven effective in encapsulating bioactive compounds. This study aimed to synthesize and characterize Cs-based microparticles containing B. microphylla fruit extract and evaluate their in vitro anti-inflammatory activity. Methods: Cs-based three-dimensional hydrogels were synthesized using physical cross-linking with ammonium hydroxide, incorporating B. microphylla fruit extract. The hydrogels were freeze-dried and mechanically ground into microparticles. The physicochemical properties of the microencapsulates were analyzed through scanning electron microscopy (SEM), optical microscopy (OM), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), and moisture absorption tests. Anti-inflammatory activity was assessed by measuring nitric oxide (NO) reduction in LPS-activated RAW 264.7 cells. Antimicrobial activity was evaluated against Staphylococcus aureus. Results: SEM and OM analyses revealed irregular morphologies with rounded protuberances, with particle sizes ranging from 135 to 180 µm. FTIR spectra indicated that no new chemical bonds were formed, preserving the integrity of the original compounds. TGA confirmed that the encapsulated extract was heat-protected. The moisture absorption test indicated the microparticles’ hydrophilic nature. In vitro, the microencapsulated extract reduced NO production by 46%, compared to 32% for the non-encapsulated extract. The microencapsulated extract was effective in reducing the microbial load of S. aureus between 15–24%. Conclusions: Cs-based microencapsulates containing B. microphylla fruit extract exhibited no chemical interactions during synthesis and demonstrated significant anti-inflammatory and antimicrobial activity. These results suggest that the Cs-based system is a promising candidate for managing inflammatory conditions.