Synthetic virus-like particles (VLP), designed from simplified building blocks, can reduce the complexity of native viral proteins and be tailored for specific applications. Using molecular dynamics simulations, we investigate the role of counterions (H2PO4-, PO43-, Cl-, and F-) in stabilizing a pre-assembled virus-like shell formed by cationic peptides exemplified by synthetic cyclopeptide (sequence: cyc-Gln-DLeu-Arg-DLeu-Arg-DLeu-Arg-DLeu) VLP shells. Our findings reveal that polyatomic anions (H2PO4- and PO43-) facilitate stable assemblies by condensing on the VLP shell to higher degrees, thereby neutralizing Coulombic repulsion among the peptide building blocks. Cohesion is largely promoted through the multidentate hydrogen bonds with arginine: Substituting arginine by lysine in the system with H2PO4- leads to destabilization of the structure. H2PO4- additionally engages in hydrophobic interactions with leucine side chains. By contrast, monoatomic anions (Cl- and F-) show insufficient coordination to the peptides and fail to stabilize the assembly, while supplementing F- with excess 1M NaCl can recover the structural integrity by screening electrostatic interactions. This study provides important insights into the role of counterions in molecular self-assembly and the nature of their interactions with amino-acid side chains involved in the cooperative formation and stabilization of synthetic virus-like shells.