To tackle the loss of activity of surfaces functionalized by coating and covalently bound molecules to materials, an intermediate system implying the noncovalent immobilization of active molecules in the inner cavity of grafted cyclodextrins (CDs) was investigated. The antifungal and antibiofilm activities of the most stable complexes of Anidulafungin (ANF; echinocandin) and thymol (THY; terpen) in various CDs were demonstrated to be almost the same as the free molecules. The selected CD was covalently bond to self-assembled monolayers on gold surfaces. The immobilized antifungal agents reduced the number of culturable Candida albicans ATCC 3153 attached to the surface by 64 ± 8% for ANF and 75 ± 15% for THY. The inhibitory activity was persistent for THY-loaded samples, whereas it was completely lost for ANF-loaded surfaces after one use. However, reloading of the echinocandin restored the activity. Using fluorescent dying and confocal microscopy, it was proposed that the ANF-loaded surfaces inhibited the adherence of the yeasts, whereas the activity of immobilized THY was found fungicidal. This kind of tailored approach for functionalizing surfaces that could allow a progressive release of ANF or THY gave promising results but still needs to be improved to display a full activity.