Candida albicans frequently causes recurrent intimal infectious disease (ID). This demands the treatment of multiple phases of the infection. The objective of this study was to uncover the host–pathogen interaction using two-dimensional (2D) epithelium cell-barrier and three-dimensional (3D) subepithelium tissue cells of human mucosa. The 2D cell cultures assessed C. albicans adhesion. Addition of the antifungal drug Fluconazol did not inhibit the adhesion, despite its pathogen growth inhibition (minimal inhibitory concentration value 0.08 μg/mL). A 3D tissue was engineered in multitranswells by placing human fibroblast cultures on a thick porous scaffold. This contained the yeast placed in the top compartment and prevented passive penetration. After 28 h, the pathogen transmigrated the barrier and was collected in the bottom compartment. A change in pathogen morphology was observed where hypha formed and grew to be 231 μm long after 28 h. The hypha was thus long enough to cross the 200 μm thick 3D tissue. The 3D infection was inhibited by addition of Fluconazol (0.08 μg/mL), confirming that penetration is dependent on pathogen growth. In conclusion, ID was reconstituted step-by-step on 2D epithelium surface and in 3D connective tissue of human mucosa. Fluconazol growth-inhibition of the pathogen C. albicans was confirmed in the 3D tissue. We thus propose that this ID in vitro test is suitable for the identification and characterization of new treatments against C. albicans.