The aim of this study was to characterize tinctures and microcapsules loaded with an ethanol extract of red propolis through chemical, physicochemical and microbiological assays in order to establish quality control tools for nutraceutical preparations of red propolis. The markers (isoflavonoids, chalcones, pterocarpans, flavones, phenolic acids, terpenes and guttiferones) present in the tinctures A and B were identified and confirmed using LC/ESI/FTMS/Orbitrap. Four compositions (A, B, C and D) were prepared to contain B tincture of the red propolis with some pharmaceutical excipients and submitted to two drying processes, i. e. spray-drying and freeze-drying to obtain microcapsules loaded with the red propolis extract. The tinctures and microcapsules of the red propolis were submitted to the total flavonoid content and antioxidant activity tests. The antibacterial activity and minimum inhibitory concentration (MIC) were tested using Staphylococcus aureus ATCC 25293 and Pseudomonas aeruginosa ATCC 27853 strains. The tinctures and microcapsules presented high flavonoid quantities from 20.50 to 40.79 mg/100 mg of the microcapsules. The antioxidant activity and IC50 were determined for the tinctures A and B (IC50: 6.95 μg/mL and 7.48 μg/mL), the spray-dried microcapsules (IC50: 8.89–15.63 μg/mL) and the freeze-dried microcapsules (IC50: 11.83–23.36 μg/mL). The tinctures and microcapsules were proved to be bioactive against gram-positive and gram-negative bacteria with inhibition halos superior to 10 mm at concentration of 200 μg/mL and MIC values of 135.87–271.74 μg/mL using gram-positive strain and 271.74–543.48 μg/mL using gram-negative strain. The tinctures and microcapsules of the red propolis have a potential application for nutraceutical products.