The electrochemically triggered dissolution of noncontinuous polyelectrolyte assemblies presenting distinct nanomorphologies and its tuning by chemical cross-linking were monitored locally, in situ, by electrochemical atomic force microscopy. Poly-l-lysine and hyaluronic acid deposited layer-by-layer on indium tin oxide electrodes at specific experimental conditions formed well-defined nanostructures whose morphologies could be easily and precisely followed along the dissolution process. In addition to shrinkage of polyelectrolyte nanodroplets, ecAFM images revealed the faster dissolution of coalesced structures compared to droplet-like complexes, and the readsorption of dissolved polyelectrolytes onto slower dissolving neighboring structures. Covalently cross-linked PLL/HA assemblies dissolved only partially, and exhibited slower dissolution rates compared to native multilayers, with a clear dependence on the cross-link density. Tuning the electrochemical dissolution of polyelectrolyte multilayers through chemical cross-linking opens new prospects for future biomedical applications, such as the development of advanced drug or gene delivery platforms allowing for tightly controlled releases of different compounds at specific rates.