Even though intergranular fracture is generally regarded as a macroscopically brittle mechanism, there are various cases where the fracture occurs at the grain boundaries with considerable plastic deformation at the macroscopic scale. There exists several microstructural reasons for grain boundaries to host crack initiation. They can interact with impurities and defects, can provide preferential location for precipitation, can behave as a source of dislocations and can impede the movement of dislocations as well. The understanding of the crack initiation and propagation at the grain boundaries requires the analysis of the grain boundary orientation and the orientation mismatch between the neighboring grains and the related the stress concentration, which is only possible through the combination of micro-mechanical plasticity and fracture mechanics. For this reason the current work studies the evolution of plasticity in three dimensional Voronoi based microstructures through a strain gradient crystal plasticity framework (see e.g. Yalcinkaya et al., 2011; Yalcinkaya et al., 2012; Yalcinkaya, 2016) and incorporates a potential based cohesive zone model (see Park et al., 2009; Cerrone et al., 2014) at the grain boundaries for the crack initiation and propagation. The numerical examples considers the effect of the orientation distribution, the grain boundary conditions, the specimen size and the fracture energy parameter on the intergranular fracture behavior of micron-sized specimens. The study presents important conclusions for the modeling of fracture at this length scale.