One of the main challenges in ligand exchange is achieving complete and uniform replacement of the original ligands. Incomplete exchange can lead to a heterogeneous surface, affecting the nanoparticle’s properties. Another challenge is the potential for ligand-induced aggregation, where the new ligands cause the nanoparticles to clump together, reducing their effectiveness. Additionally, the choice of solvent and reaction conditions must be carefully optimized to avoid degrading the nanoparticles or the ligands.