Events taking place during electrospray ionization (ESI) can trigger the self-assembly of various nanoclusters. These products are often dominated by magic number clusters (MNCs) that have highly symmetrical structures. The literature rationalizes the dominance of MNCs by noting their high stability. However, this argument is not necessarily adequate because thermodynamics cannot predict the outcome of kinetically controlled reactions. Thus, the mechanisms responsible for MNC dominance remain poorly understood. Molecular dynamics (MD) simulations can provide atomistic insights into self-assembly reactions, but even this approach has thus far failed to provide pertinent answers. The current work overcomes this limitation. We focused on salt clusters formed from aqueous NaCl solutions during ESI. The corresponding mass spectra are dominated by the Na 14 Cl 13 + MNC. Simulations of ESI droplets showed nonspecific association of Na + and Cl − , culminating in gaseous clusters via solvent evaporation to dryness (charged residue mechanism). These nascent clusters did not show any preference for MNCs. In mass spectrometry experiments, analyte ions undergo in-source activation prior to detection. We emulated in-source activation by heating nascent clusters in our MD runs. Heating triggered structural fluctuations and dissociation events, generating MNC-dominated product distributions. Why are MNCs preferred after in-source activation? Thermally excited clusters frequently adopt structures consisting of a preformed MNC and a stringlike protrusion that contains the surplus ions. Facile separation of these protrusions releases the MNC (Cluster hot → MNC-protrusion → MNC + protrusion). This work marks the first time that MD simulations were able to capture cluster self-assembly with subsequent "molecular pruning", generating MNC-dominated product distributions that agree with experiments.