This work aimed to study the evolution of the color and content of anthocyanins, carotenoids, and aroma compounds of loengo nectars (Anisophyllea boehmii Engl.) subjected to different pasteurization treatments (from 70 °C/60 min to 100 °C/15 min) and storage conditions from 4 to 45 °C for up to 35 days. Spectrophotometric, chromatographic (HPLC-DAD and HS-SPME/GC-MS) and CIE-Lab* analyses were used to monitor the evolution of pigments, color and aroma compounds over time. First-order kinetics and Arrhenius models were applied to calculate the reaction rate constants and activation energies by non-linear optimization. The results revealed that pasteurization treatments did not greatly alter the pigments except at 100 °C for carotenoids which decreased of 23% within 15 min. However, the beverage color remained quite stable during the heating step. During storage, the anthocyanin content was strongly affected decreasing between 58 and 100% in 15 days depending on the temperature. Carotenoid degradation was also significant, with losses of around 30% in 35 days below 30 °C and close to 85% at 45 °C. Consequently, the color of the pasteurized product changed quickly during storage even at room temperature. The degradation rate of anthocyanins that depended on the geographical origin of the fruit, could not be mitigated by adding ascorbic acid or by deaerating the nectar. Both pasteurization and storage strongly modified the aroma profile of the beverage, with some aroma compounds degrading and others appearing. Further investigations are required to elucidate the reaction mechanisms involved and to identify solutions for optimizing the preservation of the nutritional and organoleptic qualities of loengo nectar.