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The routine spermidine (SPD) detection method is time-consuming and laborious due to the lengthy chromatographic separation and/or tedious sample derivatization pretreatment. In this study, direct analysis in real-time ionization mode coupled with mass spectrometry (DART-MS) was developed to rapidly determine the SPD content of 12 bean cultivars. The results were compared in detail with those of the classical UHPLC-ESI-QTOF method. After conducting a series of optimizations, a simple sample extraction procedure employing 80% aqueous methanol, was followed by determination of sample extracts directly without any chromatographic separation or prior derivatization. The validated method showed excellent performance with low limits of detection (LOD of 0.025 mg·kg−1) and good recovery rates (102.79–148.44%). The investigation highlighted that the DART-MS method (~1.3 min per three samples) could be used as a high-throughput alternative to the classic UHPLC-ESI-QTOF method (~15 min per three samples).