Polyphenols, including glycosylated polyphenols, were analyzed via a procedure based on injection-port derivatization coupled to gas chromatography–tandem mass spectrometry (GC–MS/MS). The polyphenols in lyophilized fruit samples were extracted with an acidified MeOH mixture assisted by ultrasound. Samples were dried under vacuum, and carbonyl groups were protected with methoxylamine. Free hydroxyl groups were subsequently silylated in-port. Mass fragmentations of 17 polyphenol and glycosylated polyphenol standards were examined using Multiple Reaction Monitoring (MRM) as the acquisition mode. Furthermore, in-port derivatization was optimized in terms of optimal injection port temperature, derivatization time and sample: N-methyl-N-(trimethylsilyl)trifluoroacetamide (MSTFA) volume ratio. A C18 solid-phase-extraction clean-up method was used to reduce matrix effects and injection liner degradation. Using this clean-up method, recoveries for samples spiked at 1 and 10 μg/g ranged from 52% to 98%, depending on the chemical compound. Finally, the method was applied to real fruit samples containing the target compounds. The complete chromatographic runtime was 15 min, which is faster than reported for recent HPLC methods able to analyze similar compounds.