The aim of the experiment was to study the morphology of collagen-based scaffolds modified by caffeic acid, ferulic acid, and gallic acid, their swelling, and degradation rate, as well as the biological properties of scaffolds, such as antioxidant activity, hemo- and cytocompatibility, histological observation, and antibacterial properties. Scaffolds based on collagen with phenolic acid showed higher swelling rate and enzymatic stability compared to scaffolds based on pure collagen, and the radical scavenging activity was in the range 85–91%. All scaffolds were non-hemolytic and compatible with surrounding tissues. Collagen modified by ferulic acid showed potentially negative effects on hFOB cells as a significantly increased LDH release was found, but all of the studied materials had antimicrobial activity againstStaphylococcus aureusandEscherichia coli. It may be assumed that phenolic acids, such as caffeic, ferulic, and gallic acid, are modifiers and provide novel biological properties of collagen-based scaffolds. This paper provides the summarization and comparison of the biological properties of scaffolds based on collagen modified with three different phenolic acids.