Caper (Capparis spinosa) is an important food ingredient whose fresh parts, particularly the flower buds, are consumed as a starter with olives, cheese, and nuts, or are used as a component in other foods. It is one of the most popular species of aromatic plants grown in the Mediterranean zone. Fermentation makes the caper edible and affects the overall aroma as well as sensory and nutritional characteristics. This study aimed to evaluate the changes in aroma, aroma-active, and phenolic compounds of caper as affected by fermentation. Purge and trap method was used for the extraction of the aroma compounds, while gas chromatography-mass spectrometry olfactometry and Liquid chromatography coupled to diode array detection and electrospray ionization tandem mass spectrometry (LC-DAD-ESI-MS/MS) were employed for the detection of aroma-active compounds and phenolics, respectively. The results showed that the total amount of aroma compounds decreased drastically (62,616 to 21,471 mu g/kg) in fermented sample. Twelve and 10 aroma-active compounds were detected in fresh and fermented caper buds, respectively, for the first time by the application of aroma extract dilution analysis. Among these compounds, methyl isothiocyanate (flavor dilution [FD] factor = 512) in fresh caper and acetic acid (FD factor = 128) in the fermented caper had the highest FD factor. With regard to the phenolic compounds, a total of 16 components were identified in fresh and fermented capers. As observed in aroma compounds, the total phenolic concentration decreased as a result of fermentation. Two phenolic compounds being kaempferol-3-O-glucosyl-rhamnosyl-glucoside and isorhamnetin hexoside were newly identified in caper. Practical Applications Capparis spinosa is one of the most popular sources of different secondary metabolites of interest to consumers. The results of the present study showed that the fermentation process of the capers is highly influential on the neutral composition of the sample. The total concentrations of aroma and phenolic compounds were reduced by 66% and 78%, respectively, in response to fermentation process.