Resting-state functional magnetic resonance imaging (rs-fMRI) has become an increasingly popular technique. This technique can assess several features of brain connectivity, such as inter-regional temporal correlation (functional connectivity), from which graph measures of network organization can be derived. However, these measures are prone to a certain degree of variability depending on the analytical steps during preprocessing. Many studies have investigated the effect of different preprocessing steps on functional connectivity measures; however, no study investigated whether different structural reconstructions lead to different functional connectivity metrics. Here, we evaluated the impact of different structural segmentation strategies on functional connectivity outcomes. To this aim, we compared different metrics computed after two different registration strategies. The first strategy used structural information from the 3D T1-weighted image (unimodal), while the second strategy implemented a multimodal approach, where an additional registration step used the information from the T2-weighted image. The impact of these different approaches was evaluated on a sample of 58 healthy adults. As expected, different approaches led to significant differences in structural measures (i.e., cortical thickness, volume, and gyrification index), with the maximum impact on the insula cortex. However, these differences were only slightly translated to functional metrics. We reported no differences in graph measures and seed-based functional connectivity maps, but slight differences in the insula when we compared the mean functional strength for each parcel. Overall, these results suggested that functional metrics are only slightly different when using a unimodal compared to a multimodal approach, while the structural output can be significantly affected.