Grain boundary engineering (GBE) has been carried out in nickel-based Alloy 690 with different initial grain sizes. The microstructure evolution during GBE-processing is characterized using electron backscatter diffraction to study the initial grain size effects on the grain boundary network (GBN). The microstructures of the partially recrystallized samples revealed that the GBE-processing is a strain-recrystallization process, during which each grain-cluster is formed by “multiple twinning” starting from a single recrystallization nucleus. Taking into consideration the coincidence site lattices (CSLs) and ∑, which is defined as the reciprocal density of coincidence sites, a high proportion of low-∑ CSL grain boundaries (GBs) and large grain-clusters are found to be the features of GBE-processed GBN. The initial grain size has a combined effect on the low-∑ CSL GBs proportion. A large initial grain size reduces the number of recrystallization nuclei that form, increasing the cluster size, but decreasing twin boundary density. On the other hand, smaller initial grain sizes increase the density of twin boundary after recrystallization, while decreasing grain-cluster size. Neither the grain-cluster size nor the twin boundary density is the sole factor influencing the proportion of low-∑ CSL GBs. The ratio of the grain cluster size over the grain size governs the proportion of low-∑ CSL GBs.