A phase transition within the ligand shell of core/shell quantum dots is studied in the prototypical system of colloidal CdSe/CdS quantum dots with a ligand shell composed of bound oleate (OA) and octadecylphosphonate (ODPA). The ligand shell composition is tuned using a ligand exchange procedure and quantified through proton NMR spectroscopy. Temperature-dependent photoluminescence spectroscopy reveals a signature of a phase transition within the organic ligand shell. Surprisingly, the ligand order to disorder phase transition triggers an abrupt increase in the photoluminescence quantum yield (PLQY) and full-width at half-maximum (FWHM) with increasing temperature. The temperature and width of the phase transition show a clear dependence on ligand shell composition, such that QDs with higher ODPA fractions have sharper phase transitions that occur at higher temperatures. In order to gain a molecular understanding of the changes in ligand ordering, Fourier transform infrared and vibrational sum frequency generation spectroscopies are performed. These measurements confirm that an order/disorder transition in the ligand shell tracks with the photoluminescence changes that accompany the ligand phase transition. The phase transition is simulated through a lattice model that suggests that the ligand shell is well-mixed and does not have completely segregated domains of OA and ODPA. Furthermore, we show that the unsaturated chains of OA seed disorder within the ligand shell.