Inflammatory bowel disease (IBD) is a chronic recurrent inflammatory disease, and the treatment of IBD remains a challenge due to its limited therapeutic efficiency, high side effects, and high cost. It has been demonstrated that sporopollenin microcapsules derived from a variety of pollen species could function as efficient drug carriers due to their great thermal stability, resilience to harsh chemicals, homogeneity in size, and biocompatibility. Herein, we engineered a biohybrid nanozyme-based edible sporopollenin system, which can be applied to effectively treat IBD. The biohybrid sporopollenin (CeNP-P) loaded with a cerium oxide nanozyme (CeNP) was encapsulated in microspheres (CeNP-P/MS) by a microfluidic electrospray technique. This micronanosystem protects the CeNP-P from degradation in gastric conditions and enables the rapid release of CeNP-P in the intestine. The released CeNP exhibited the desired anti-inflammatory effects by suppressing pro-inflammatory cytokines and scavenging reactive oxygen species. To explore its practical value, in vivo experiments have been carried out with an IBD mouse model. Compared to the IBD group, the treatment groups displayed significant therapeutic outcomes, particularly the CeNP-P/MS group. Following taking CeNP-P/MS orally, key IBD symptoms were greatly alleviated, as evidenced by the restored colonic morphology, enhanced intestinal barrier integrity, and induced inflammatory responses. Collectively, these findings demonstrate that the present edible system can offer a promising strategy for the effective treatment of intestinal diseases.