Given the paramount importance of agricultural products in global health and food security, and the increasing consumer demand, understanding the mechanical behavior of these materials under various conditions is necessary yet challenging. Due to their heterogeneous and non-uniform nature, determining their mechanical behavior is complex. This study employs atomic force microscopy (AFM) to determine the modulus of elasticity of limequat fruit at the microscopic scale and compares it with macroscopic methods. The analyses revealed a statistically significant difference (at the 1% level) in the mechanical behavior determined at the macroscopic scale. The highest modulus of elasticity, 0.752 MPa, was observed using Hertz's theory under complete placement between two parallel planes. The lowest, 0.059 MPa, was noted when a spherical probe compressed a rectangular sample. The average modulus of elasticity of the limequat peel was 2.007 MPa. At the microscopic scale, the modulus of elasticity of the fruit tissue ranged from 0.370 to 0.365 MPa, and for the peel, it was 0.246 MPa. RESEARCH HIGHLIGHTS: Working principles of this innovative technique were elaborated. The AFM technique used provide elasto-mechanical properties determination of cell walls of single living cells extracted from biological materials on the nanoscale. By combining AFM topographical image and nano-indentation of living fruit cells it will be possible to investigate cells' elasto-mechanical properties. Atomic force microscopy holds great potential for monitoring fruit mechanical properties of biological materials.