Aim: Distinction of species within the Candida glabrata complex (i.e., C. glabrata sensu stricto, Candida nivariensis and Candida bracarensis) is relevant for epidemiological purposes and antifungal management. Materials & methods: Two commercial matrix-assisted laser desorption ionization–time of flight mass spectrometry systems were comprehensively evaluated for the identification of fungi within this complex. Results: None of the species (C. nivariensis and C. bracarensis) were identified correctly by Vitek mass spectrometry (MS^®) v2.0 In Vitro Diagnosis system and Bruker Biotyper MS^® v3.1, but all were correct by the Vitek MS^® Research Use Only system. The Bruker ClinProTools software showed 100% recognition capability and cross validation for the discrimination of C. nivariensis and C. bracarensis. Conclusion: Using Vitek MS Research Use Only and Bruker ClinProTools can overcome limitations of the Vitek MS In Vitro Diagnosis and Bruker Biotyper databases in the identification of C. glabrata complex.