The twin-arginine protein translocation (Tat) system transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membrane of chloroplasts. The Escherichia coli Tat system comprises TatC and two additional sequence-related proteins, TatA and TatB. Tat-directed proteins are distinguished by a conserved twin-arginine (RR-) motif in their signal sequences. Substrate binding promotes a conformation rearrangement of the Tat complex. TatA is then recruited to the substrate activated TatBC complex, where it polymerizes to form the substrate translocation pathway. The central challenge in understanding Tat transport is to determine how the Tat components are assembled to form the active translocon allowing folded substrates to be transferred across the membrane bilayer. In this work, we used molecular dynamics simulations to describe the TatA oligomerization mechanism and how the translocation pathway is formed. Our results show that the Tat complex becomes more dynamic after substrate binding. The presence of the substrate induces a “breathing” movement, increasing the separation between two adjacent TatC subunits. Moreover, our results also suggest that substrate binding induces an asymmetry in the Tat Complex, favouring TatA aggregation around the interface opposite to the TatC subunit where the signal peptide is bound. The TatA oligomer is anchored to the Tat complex through contacts with the TM1 and the TM6 of the adjacent TatC subunits, which promotes a local weakening of the membrane bilayer. Our extensive coarse-grained MD simulations provide a molecular description of the Tat translocon assembly and new insights into the Tat transport cycle.