This study presents a novel multifunctional gel prepared using Chlorella protein (CP) to extend the shelf life of perishable fruits like cherries. Structural, rheological, and scanning electron microscopy analyses revealed that CP hydrogels possess excellent solid-like properties and a stable porous structure. The water-holding capacity (WHC) improved significantly from 67.11 ± 0.72% to 96.53 ± 0.61% with increasing CP concentration, indicating enhanced WHC. Additionally, the decomposition temperature at 5% weight loss was 150°C, demonstrating good thermal stability. Due to the ionization of -COOH and -NH2 groups, the CP hydrogel showed excellent pH sensitivity, with low dissolution rates in acidic environments (64.97%) and significantly higher rates in alkaline environments (448.50%). Furthermore, the CP hydrogel inhibited the penetration of Staphylococcus aureus and Escherichia coli, with increased resistance at higher CP concentrations. CP-22.5 reduced bacterial counts from 109 to less than 105 CFU. Its DPPH and ABTS•+ radical scavenging capacities were 74.50% and 97.92%, respectively, indicating strong antioxidant properties. In cherries preservation tests, CP hydrogel extended preservation time to 15 days compared to 5 days in the control group, effectively inhibiting decay, suggesting CP hydrogel is a promising choice for multifunctional fruit preservation.