Currently, demand for functional foods is increasing in the public interest in order to improve life expectations and general health. Food matrices containing probiotic microorganisms and active compounds encapsulated into carrier agents are essential in this context. Encapsulation via the lyophilisation method is widely used because oxidation reactions that affect physicochemical and nutritional food properties are usually avoided. Encapsulated functional ingredients, such as quercetin and Bacillus clausii, using two carrier agents’ matrices—I [inulin (IN), lactose (L) and maltodextrin (MX)] and II [arabic (A), guar (G), and xanthan (X) gums)]—are presented in this work. A D-optimal procedure involving 59 experiments was designed to evaluate each matrix’s yield, viability, and antioxidant activity (AA). Matrix I (33.3 IN:33.3 L:33.3 MX) and matrix II (33.3 A:33.3 G:33.3 X) exhibited the best yield; viability of 9.7 log10 CFU/g and 9.73 log10 CFU/g was found in matrix I (using a ratio of 33.3 IN:33.3 L:33.3 MX) and matrix II (50 G:50 X), respectively. Results for the antioxidant capacity of matrix I (100 IN:0 L:0M X) and matrix II (0 A:50 G:50 X) were 58.75 and 55.54 (DPPH* scavenging activity (10 µg/mL)), respectively. Synergy between matrices I and II with use of 100IN:0L:OMX and 0A:50G:50X resulted in 55.4 log10 CFU/g viability values; the antioxidant capacity was 9. 52 (DPPH* scavenging activity (10 µg/mL). The present work proposes use of a carrier agent mixture to produce a functional ingredient with antioxidant and probiotic properties that exceed the minimum viability, 6.0 log10 CFU/g, recommended by the FAO/WHO (2002) to be probiotic, and that contributes to the recommended daily quercetin intake of 10–16 mg/day or inulin intake of 10–20 g/day and dietary fibre intake of 25–38 g per day.