A way to understand kinetics and explore mechanism of reactions is to identify the intermediates and their relative energetics. In this respect, low-energy electrospray ionization mass spectrometry is providing information on possible intermediates that can be tandemly verified using crystallography of the products. This has been extended to the study of the formation of functional clusters of transition metals under varying conditions. The reaction of NiL2 (L = 2-ethoxy-6-( N-methyliminomethyl)phenolate) with MII(H2O)6(ClO4)2 in the presence of Et3N base leads to [Ni xM7- x(μ3-OH)6L6]2+ according to NiL2 → [M2L3]+ → [M4(OH)2L4]2+ → [M7(OH)6L6]2+. In contrast, its reaction with MII(H2O)6(NO3)2 in the absence of base leads to two crystallographic structural types [MII3L4(NO3)2(H2O)2]·CH3CN for M = Ni (I-Ni3) or Co (I-Co xNi3- x, x = 0-3) and [MIINiII2L4(NO3)2] for M = Zn (II-ZnNi2) or Co (II-CoNi2). Interestingly, ESI-MS suggests three slightly different formation processes: for I-Ni3, {NiL2 → [Ni2L(NO3)2]+ → [Ni2L2(NO3)]+ → [Ni2L3]+ → [Ni3L4(NO3)]+}; for II-ZnNi2, {NiL2 → [ZnNiL2(NO3)]+ → [ZnNi2L4(NO3)]+}; for II-CoNi2 and I-Co xNi3- x, {NiL2 → [M2L2(NO3)]+ → [M2L3]+ → [M3L4(NO3)]+}. Magnetization measurements reveal the site of each metal ionin II-ZnNi2 and the number of single electrons within different clusters. Without the base, there is an interplay between the weak coordinating nitrate and water stabilizing the two structural types via the different formation processes. The results indicate that not only the strength of the ligand matters but also the ionic sizes and possibly softness of the metals may be implicated.