Enniatins (ENN) and beauvericin (BEA) are emerging mycotoxins that have been traditionally determined by liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS). However, to the best of our knowledge, no analytical methods based on capillary electrophoresis (CE)–MS/MS have been reported so far. Due to their non-polar nature, in this work, a non-aqueous CE (NACE) method coupled to quadrupole time-of-flight–MS is proposed for the first time to identify and quantify these mycotoxins. Determination was achieved in 4 min under optimum conditions: 40 mM ammonium acetate in 80:20 (v/v) acetonitrile-methanol (buffer), 30 kV (voltage), 80 cm (capillary length), 20 °C (capillary temperature) and 50 mbar × 30 s (injection). Higher selectivity can be achieved when compared with LC due to the formation of exclusive CE adducts such as [M + CH3CH2NH3]+. “All Ions” acquisition mode was selected as it allows the quantification of the usual ENNs, as well as the identity confirmation of less common ENNs.The method was validated for wheat samples, obtaining limits of quantification from 4.0 to 8.3 μg/kg depending on the emerging mycotoxin, recovery values higher than 87.4%, and intra- and inter-day precision values (RSDs) lower than 15.1% in all cases. Finally, 29 wheat samples were analyzed, finding 26 samples with concentrations of enniatin B higher than the limit of quantification (7.5–1480 μg/kg), 20 for enniatin B1 (5.2–550 μg/kg), 7 for enniatin A (10–55 μg/kg), 4 for enniatin A1 (12.6–77 μg/kg) and 5 for BEA (9.2–16.4 μg/kg). Moreover, two other ENNs were tentatively identified.