A series of six examples of 1,1-difluoro-3,5-diaryl-1H [1,2,3,5] oxadiazaborinino[3,4-a]quinoxalin-11-ium-1-uides as a new N-quinoxaline-based boron complex with variable structures was synthesized at 65–70% yields from the reaction of the respective N-(3-arylquinoxalin-2-yl)benzamides with BF3·Et2O — in which aryl = phenyl, 4-ClC6H4, 4-CH3C6H4, and 4-NMe2C6H4. All new benzamides and BF2-complexes were fully characterized by 1H-, 13C, 19F-, and 11B-NMR spectroscopy and single-crystal X-ray diffraction. Moreover, the photophysical properties, TD-DFT analysis, DNA and BSA-binding experiments, and molecular docking studies for these new organoboron complexes were studied. The new BF2-heterocycles demonstrated to be weak generators of 1O2, although their solutions at 5.0 µM showed great photostability over the investigated irradiation. Additionally, the results of the DNA and BSA-binding studies indicated that the greatest interactions were selective in the minor groove of DNA and by the tryptophan site in the BSA albumin pocket.