The emergence of resistant
Candida albicans
has made clinical fluconazole (FLC) treatment difficult. Improving sensitivity to FLC is an effective way to treat resistant isolates. Berberine hydrochloride (BBH) is a commonly used traditional Chinese medicine with antimicrobial effects, especially in resistant isolates. We investigated the molecular mechanisms underlying BBH and FLC synergism on biofilm-positive FLC-resistant
C. albicans
inhibition. Checkerboard microdilution assays and time-kill assays showed a strong synergistic effect between BBH and FLC in resistant
C. albicans
isolates, causing a significant 32–512-fold reduction in minimum inhibitory concentrations. BBH combined with FLC inhibited intracellular FLC efflux due to key efflux pump gene
CDR1
downregulation, whereas FLC alone induced high
CDR1
transcription in resistant strains. Further, BBH + FLC inhibited yeast adhesion, morphological hyphae transformation, and biofilm formation by downregulating the hyphal-specific genes
ALS3
,
HWP1
, and
ECE1
. BBH caused cytoplasmic Ca
2+
influx, while FLC alone did not induce high intracellular Ca
2+
levels. The vacuolar calcium channel gene
YVC1
was upregulated, while the vacuolar calcium pump gene
PMC1
was downregulated in the BBH + FLC and BBH alone groups. However, vacuolar calcium gene expression after FLC treatment was opposite in biofilm-positive FLC-resistant
C. albicans
, which might explain why BBH induces Ca
2+
influx. These results demonstrate that BBH + FLC exerts synergistic effects to increase FLC sensitivity by regulating multiple targets in FLC-resistant
C. albicans
. These findings further show that traditional Chinese medicines have multi-target antimicrobial effects that may inhibit drug-resistant strains. This study also found that the vacuolar calcium regulation genes
YVC1
and
PMC1
are key BBH + FLC targets which increase cytoplasmic Ca
2+
in resistant isolates, which might be critical for reversing biofilm-positive FLC-resistant
C. albicans
.