The brain’s functional networks can be assessed using imaging techniques like functional magnetic resonance imaging (fMRI) and electroencephalography (EEG). Recent studies have suggested a link between the dynamic functional connectivity (dFC) captured by these two modalities, but the exact relationship between their spatiotemporal organization is still unclear. Since these networks are spatially embedded, a question arises whether the topological features captured can be explained exclusively by the spatial constraints. We investigated the global structure of resting-state EEG and fMRI data, including a spatially informed null model and found that fMRI networks are more modular over time, in comparison to EEG, which captured a less clustered topology. This resulted in overall low similarity values. However, when investigating the community structure beyond spatial constraints, this similarity decreased. We show that even though EEG and fMRI functional connectomes are slightly linked, the two modalities essentially capture different information over time, with most but not all topology being explained by the underlying spatial embedding.