Isotropic conductive adhesives (ICAs) are promising candidates for low temperature joining technologies in microelectronics, enabling ultra-fine pitch sizes. Especially in solar and automotive applications, long-term reliability is a prerequisite in new generation electronics. It is essential that reliability predictions take processing history into account in order to correctly address premature failures as well as to make sound long-term predictions. In this paper, residual stresses that develop in a nano-Ag ICA interconnect during the assembly of a flip-chip pin grid array are investigated. A multiscale modeling framework is adopted to link the nano-sized particles to the interconnect level. This is achieved by the numerical analysis of the mechanical response during the curing process through the computational homogenization approach, in which two boundary value problems, one at each scale are formulated and solved simultaneously, in a fully nested manner. The mechanical response of the interconnect is analyzed with respect to the particle volume fraction and distribution properties. It is shown that, although the overall residual stresses at the interconnect scale decrease with increasing the amount of conductive particles, at the particle scale local stress concentrations increase, indicating the possibility of damage and decohesion that might compromise mechanical integrity and interrupt the conductive path. Hence, the multiscale scheme proved crucial for the sound analysis of the nano-particle ICA interconnect problem, where consideration of only the interconnect level would lead to misleading conclusions.