This study investigates the corrosion inhibition effects of eco-friendly conifer cone extract (CCE) on steel rebars embedded in cement mortar exposed to 3.5% NaCl under alternate wet/dry cycles. CCE concentrations of 0, 0.5, 1.0, 1.5, and 2.0% (denoted CCM0 to CCM4) were tested. Electrochemical and weight loss analyses revealed that 0.5% CCE significantly enhanced corrosion resistance, achieving 84.8% inhibition efficiency via polarization methods and a reduced corrosion rate of 9.46 mmpy. Chloride-binding studies indicated that 0.5% CCE improved adsorption intensity and multilayer adsorption constants compared to those of the control, as confirmed by Freundlich and Harkins-Jura isotherms. Surface analyses using SEM/EDS and AFM demonstrated the formation of a dense, protective passive layer on steel rebar surfaces, effectively reducing the surface roughness to 41.05 nm in CCM1 specimens. Theoretical simulations using SCC-DFTB and molecular dynamics showed a strong interaction between CCE functional groups and the iron surface, supporting experimental findings. Mechanical and porosity evaluations confirmed that 0.5% CCE maintained compressive strength and permeability while improving corrosion resistance. These results position CCE as a cost-effective, eco-friendly inhibitor with potential applications in protecting reinforced concrete structures in chloride-rich environments.