We describe phase transitions in assemblies of octanethiol (OT)-capped nanoclusters of Ag and Au and CdS of sizes ranging from 2 to 5 nm, created by a new variant of the Brust synthesis method, without the use of phase transfer agents. We probed the stability of these assemblies by a combination of UV-Visible spectrometry, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and in situ polarized microscopy (PLM). Our results show that Ag nanoclusters form a crystalline assembly at ambient temperatures. Upon heating, these assemblies undergo two reversible phase transitions corresponding to melting of (i) a phase comprised of excess thiols that are not linked to the nanoclusters, and (ii) the nanocluster assembly, at ∼60 and 124 °C, respectively. In contrast, Au nanocluster assemblies are softer, waxy solids, and show sub-zero melting transitions. Both these assemblies show no observable mass loss up to ∼180 °C. Cds nanocluster assemblies are also waxy solids, but show a nonreversible melting transition at 137 °C, with simultaneous mass loss due to OT desorption. From our results the thermal stability of the nanoclusters was OT-Ag > OT-Au > OT-CdS.