Natural climatic conditions have significant negative impacts on the long-term mechanical properties and dimensional stability of bio-based concrete considering the high water absorption of bio-aggregates and corresponding biodegradations. In this study, the effects of three hydrophobic treatments (integral mixing, aggregate coating, concrete coating) on the physical properties, mechanical strengths, and drying shrinkage characteristics of bio-based peach kernel shell concrete in real climatic natural environments are investigated. Results show that bio-based peach kernel shell concrete has lower mechanical strength in outdoor climatic conditions than in indoor standard curing conditions. The swelling and shrinkage process causes the visible microcrack and debonding between bio-based materials and mortar interface. The drying shrinkage of bio-based peach kernel shell concrete in outdoor conditions is highly dependent on real climatic environments, including temperature, humidity and rainfall. The hydrophobic surface-coated concrete exhibits excellent resistance to real climatic environments, as well as good mechanical strength and dimensional stability, with 15.7% less drying shrinkage in 18 months, compared to reference concrete. Moreover, cellulose and hemicellulose of heat-treated bio-aggregates do not degrade over time in outdoor conditions due to the enhanced biodegradation resistance. The hydrophobic surface coating treatment is recommended for enhancing the service life of bio-based peach kernel shell concrete in real climatic environments.