Reference broth microdilution protocols for the antifungal susceptibility testing (AST) of yeasts are available, but routine AST relies more on simpler alternatives. In this work, the Etest and a novel flow cytometry (FC) method were compared to the Clinical Laboratory Standards Institute (CLSI) protocol M27-A3. Caspofungin and anidulafungin were tested against 60 clinical isolates of Candida glabrata, C. krusei, and C. parapsilosis. There were two intermediate susceptibility results and 19 out of 20 tested C. krusei strains were categorized as resistant to caspofungin (minimum inhibitory concentration [MIC] of 1.0 mg/L). There was a generally excellent essential agreement with the reference method, only interrupted by Etest results for the anidulafungin susceptibility of C. glabrata (80%) and the FC method's results for caspofungin with C. krusei (40%). Categorical agreements were excellent, with the notable exception of the caspofungin-resistant C. krusei, with 19 very major errors for the FC method and 19 minor errors plus one very major error for the Etest (5% and 0% categorical agreements, respectively). Two additional minor errors were registered for the FC method when testing C. parapsilosis with anidulafungin and caspofungin. Overall, these data come to question the suitability of recently approved clinical breakpoints in the case of C. krusei. Further studies including fks mutants are now required.