Cyclodextrins (CDs) are natural cyclic oligosaccharides with the ability to form inclusion complexes with various organic substances. In this paper, we investigate the potential of CD complex formation to enhance the antibacterial activity and antioxidant properties of poorly soluble bioactive agents, such as chalcones, chromenes, stilbenoids and xanthylium derivatives, serving as potential adjuvants, in comparison with standard antiseptics. The interaction of these potential adjuvants with the hydrophobic pocket of methyl-β-cyclodextrin (MCD) was confirmed using spectroscopic methods such as UV-vis, FTIR, and 1H NMR. These complexes, when used in combination with metronidazole, showed a synergy coefficient of 1.36 for chalcones, presumably, via efflux pump inhibition in bacterial cells. To explore the possibility to create theranostic formulation, we used fluorescent markers to visualize target cells, antiseptics to provide antibacterial activity, and natural bioactive agents as chalcones that act as adjuvants. Additionally, new antioxidant compounds were found such as Xanthylium derivative (R351) and 1-methyl-3-(2-amino-3-cyano-7-methoxychromene-4-yl)-pyridinium methanesulfate: the pronounced antioxidant properties of these substances are observed comparable to quercetin in the efficiency. Rhodamine 6G, gentian violet and Congo Red exhibit good antioxidant properties, although its activity is an order of magnitude lower than that of quercetin. However, they have remarkable potential due to their multifaceted nature, including the ability to visualize target cells. The most effective theranostic formulation is the combination of the main drug (metronidazole) + dye/fluorophore (methylene blue / rhodamine 6G) for visualization of target cells + adjuvant (chalcones or xanthylium derivatives) for antiinflammation effect. Formulation options using antiseptics are possible for local use. The presented formulas demonstrate therapeutic potential, allowing simultaneous visualization and therapeutic effect.