Cu-Cu direct interconnects are highly desirable for the microelectronic industry as they allow for significant reductions in the size and spacing of microcontacts. The main challenge associated with using Cu is its tendency to rapidly oxidize in air. This research paper describes a method of Cu passivation using a self-assembled monolayer (SAM) to protect the surface against oxidation. However, this approach faces two main challenges: the degradation of the SAM at room temperature in the ambient atmosphere and the monolayer desorption technique prior to Cu-Cu bonding. In this paper, the systematic investigation of these challenges and their possible solutions are presented. The methods used in this study include thermocompression (TC) bonding, X-ray photoelectron spectroscopy (XPS), shear strength testing, scanning electron microscopy (SEM), and energy dispersive X-ray spectroscopy (EDX). The results indicate nearly no Cu oxidation (4 at.%) for samples with SAM passivation in contrast to the bare Cu surface (27 at.%) after the storage at −18 °C in a conventional freezer for three weeks. Significant improvement was observed in the TC bonding with SAM after storage. The mean shear strength of the passivated samples reached 65.5 MPa without storage. The average shear strength values before and after the storage tests were 43% greater for samples with SAM than for the bare Cu surface. In conclusion, this study shows that Cu-Cu bonding technology can be improved by using SAM as an oxidation inhibitor, leading to a higher interconnect quality.