Five different wines (standard Graševina, macerated Graševina with and without sulfur, rosé, and standard Plavac Mali), all typical Croatian wines, were tested to determine the antimicrobial activity against two Escherichia coli bacterial strains (ATCC® 25922 and ATCC® 8739) in vitro and using sea bass (Dicentrarchus labrax) fillets as food matrix. The chemical composition of wines (pH, acidity, alcohol, total phenolics, anthocyanins, tannins, and sulfur content) and antimicrobial activity (minimal inhibitory concentration (MIC), agar-well diffusion method) were determined. The total phenolic content of the wines ranged from 305–3210 mg gallic acid equivalents per liter (GAE/L), and did not correlate to antimicrobial activity. The two wines with the lowest phenolic content (standard Graševina and rosé) had the lowest MIC values (122 and 429 mg GAE/L). A specific relation between the winemaking process and a particular MIC value was not established. There was also no relation found between the pH value, ethanol content, sulfur, or phenolics in regards to the antimicrobial effect. In fish fillets marinated in wine + water mixture (v/v = 1:1) and inoculated with 7 log colony forming units (CFU)/25 g the growth of bacteria was reduced after three days of storage at 4 °C. Subsequent storage resulted in the growth of bacteria in all samples, with the lowest growth of E. coli ATCC® 25922 in macerated Graševina and E. coli ATCC® 8739 in standard Graševina. All wines showed the capacity to reduce the number and growth of heavily infected sea bass filets, but correlation with specific wine constituents was not found. Taking into account the numerous reactive mechanisms between food and wine, all in vitro studies in controlled laboratory conditions should be further verified in the relevant environment, and additional research is needed to clarify the role of individual wine components in the mechanism of antimicrobial activity.