In this work, two different capillary electrophoresis-mass spectrometry (CE-MS) methods, namely, capillary electrophoresis-ion-trap mass spectrometry (CE-IT-MS) and capillary electrophoresis-time-of-flight mass spectrometry (CE-TOF-MS), applied to analyze biogenic amines in wine samples are investigated. A group of five amines was selected as case study (namely, putrescine, cadaverine, histamine, phenylethylamine and tyramine) since they are the most frequently biogenic amines found in wines. The possibilities of both instruments in terms of sensitivity, selectivity and quantitation during the determination of the mentioned biogenic amines in wine samples was studied and their results corroborated by HPLC. After optimization of the analytical conditions, CE-IT-MS and CE-TOF-MS allowed the identification of biogenic amines in wines without any previous treatment except diluting 1:1 with water and filtering. Biogenic amines were determined in three red wines and one white wine showing, as expected, a higher concentration in red wines. Moreover, CE-IT-MS and CE-TOF-MS were compared regarding their capacity to detect other biogenic amines different to the selected ones in wine samples, showing CE-TOF-MS a much better capability (i.e., putrescine, cadaverine, histamine, phenylethylamine, tyramine, triptamine, spermidine, spermine, ethanolamine and isoamylamine were identified by CE-TOF-MS in a single analysis). Moreover, CE-TOF-MS allowed the quantitation of biogenic amines with limits of detection as low as 10 ng/mL, comparable to those obtained using HPLC with fluorescence detection, without any previous derivatization step and with analysis times fivefold faster (40 min by HPLC and 8 min by CE-TOF-MS).