The elastic and plastic mechanical properties of intermetallic compound (IMC) phases of a lead-free Sn3.5Ag/Cu-substrate soldering system are investigated in different sized joints using nano-indentation. The specimens were prepared using solid–liquid interdiffusion soldering process with joint sizes ranging from 15 to 450 μm. Solder joints were subjected to 360 °C soldering temperature for 20 min and then air cooled to room temperature to create testable IMCs thicknesses. Nano-indentation was used to extract the elastic and plastic properties of Cu6Sn5, Cu3Sn, and Ag3Sn IMCs and β-tin and copper materials. Cu–Sn IMCs formed in specimens with smaller joint size show higher elastic modulus, hardness, and yield strength and lower work hardening exponent. This was attributed to the dimensional constraints associated with decreasing joint size and the local stresses developed during fabrication in joints with different sizes. Local elastic modulus and hardness of single grains of Cu6Sn5 were obtained using a combination of nano-indentation and electron backscatter diffraction (EBSD) techniques. Grains with c-axis at a 45 deg angle with respect to the nano-indentation loading direction show higher elastic modulus (∼8.70% higher) and hardness (8.85% higher) compared to the grains that have a c-axis that is almost perpendicular to the nano-indentation loading direction.