Staphylococci growing in the form of biofilm exhibit high resistance to a plethora of antibiotics. The aim of the study was to assess the influence of ethanolic extract of propolis (EEPs) on S. epidermidis ATCC 35984 biofilm using fluorescent microscopy. Propidium iodide (PI) and SYTO 9 were used for differentiation of live and dead cells, and calcofluor white was used to stain the extracellular matrix, the self-produced extracellular polymeric substances (EPS). The outcomes of the research confirm the promising potential of EEPs for eradication of staphylococcal biofilm. However, its activity cannot be classified as fully satisfactory, either in terms of the effectiveness of elimination of bacterial cells or disturbing the EPS structure. A two or even four times higher concentration of EEPs compared to MIC (Minimum Inhibitory Concentration) against planktonic cells (128 µg/mL) was necessary for effective (estimated for 90%) elimination of living cells from the biofilm structure. Unfortunately, even at that concentration of EEPs, the extracellular matrix was only partially disturbed and effectively protected the residual population of living cells of S. epidermidis ATCC 35984. In our opinion, a combination of EEPs with agents disrupting components of EPS, e.g., proteases, lysines, or enzymes degrading extracellular DNA or PIA (polysaccharide intercellular adhesin).