Polyelectrolyte complexes (PECs), formed via the self-assembly of oppositely charged polysaccharides, are highly valued for their biocompatibility, biodegradability, and hydrophilicity, offering significant potential for biotechnological applications. However, the complex nature and lack of insight at a molecular level into polyelectrolytes conformation and aggregation often hinders the possibility of achieving an optimal control of PEC systems, limiting their practical applications. To address this problem, an in-depth investigation of PECs microscopic structural organization is required. In this work, for the first time, a hybrid approach that combines experimental techniques with atomistic molecular dynamics simulations is used to elucidate, at a molecular level, the mechanisms underlying the aggregation and structural organization of complexes formed by gellan and chitosan, i.e. PECs commonly used in food technology. This combined analysis reveals a two-step complexation process: gellan initially self-assembles into a double-helix structure, subsequently surrounded and stabilized by chitosan via electrostatic interactions. Furthermore, these results show that complexation preserves the individual conformation and intrinsic functionality of both polyelectrolytes, thereby ensuring the efficacy of the PECs in biotechnological applications.