The volatile components emitted by fresh aromatic flowers of Plumeria rubra L., harvested in southern Ecuador during three different months were determined to evaluate the fluctuation of secondary metabolites. The volatile compounds were analyzed using headspace solid-phase microextraction (HS-SPME) followed by gas chromatography coupled to mass spectrometry (GC-MS) and a flame ionization detector (GC-FID) using two types of columns: a non-polar (DB-5ms) and polar column (HP-INNOWax). The principal chemical groups were hydrocarbon sesquiterpenes (43.5%; 40.0%), oxygenated sesquiterpenes (23.4%; 26.4%), oxygenated monoterpenes (14.0%; 11.2%), and hydrocarbon monoterpenes (12.7%; 9.3%). The most representative constituents were (E,E)-α-Farnesene (40.9-41.2%; 38.5-50.6%), (E)-nerolidol (21.4-32.6%; 23.2-33.0%), (E)-β-ocimene (4.2-12.5%; 4.5-9.1%), (Z)-dihydro-apofarnesol (6.5-9.9%; 7.6-8.6%), linalool (5.6-8.3%; 3.3-7.8%), and perillene (3.1-5.9%; 3.0-3.2%) in DB-5ms and HP-INNOWax, respectively. Finally, we reported for the first time the enantiomeric distribution of P. rubra flowers, where the enantiomers (1R,5R)-(+)-α-pinene, (S)-(-)-limonene, (S)-(+)-Linalool, and (1S,2R,6R,7R,8R)-(+)-α-copaene were present as enantiomerically pure substances, whereas (S)-(+)-(E)-Nerolidol and (R)-(+)-(E)-Nerolidol were observed as scalemic mixtures. This study provides the first comprehensive and comparative aroma profile of Plumeria rubra cultivated in southern Ecuador and gave us a clue to the variability of P. rubra chemotypes depending on the harvesting time, which could be used for future quality control or applications in phytopharmaceutical and food industries.