Mesoscale organization of transcription is thought to play an important role in its regulation, with numerous factors forming biomolecular condensates that interact with the C-terminal domain (CTD) of RPB1, the largest subunit of RNA polymerase II (RNAPII). However, in situ imaging of these transient transcriptional condensates within the nucleus remains challenging and their structural organization is largely uncharacterized due to their small size and inherently dynamic nature. We used comprehensive biochemical analyses, single particle cryo-EM structure determinations, cryo-ET reconstitutions, in vivo validations, and coarse-grained simulations to study the molecular structure of a condensate containing the phosphorylated RNAPII elongation complex and the elongation factor RECQ5. Through this integrative approach, we reconstructed the full structure of this transcriptional condensate model, uncovering critical interactions that provide insight into the mechanisms underlying RNAPII condensation with scaffolding factors. We show that RECQ5 forms a condensate scaffold matrix, integrating the elongation complex of RNAPII through a network of site specific interactions, reinforcing the condensate’s structural integrity. We also show that not only the hyperphosphorylated CTD, but also the entire RNAPII, including the transcribing core, are embedded within the condensates, addressing the key question of the spatial arrangement of transcriptional condensates.