The objective of this work was to optimize the incorporation of citric acid (CA) in the gastroretentive microballoons containing riboflavin (RF) in order to achieve dual controlled release system and consequently enhance the bioavailability of RF. Microballoons of 739 ± 1.9 µm containing RF-CA were prepared by modified emulsion solvent diffusion method and were evaluated both for in vitro and in vivo performance. RF-CA microballoons with 22.8% RF and 37.2% CA entrapped in the shell matrix composed of Eudragit® S 100 and HPMCK4M and in vitro buoyancy of 86.0 ± 0.88% (RCM3) was selected for further studies. RCM3 exhibited biphasic, pH-dependent in vitro dual controlled release of RF (0.9933-0.9962) and CA (0.996-0.9984) beyond 1 h in both simulated fasted and fed state conditions. RCM3 was able to achieve higher mean plasma concentrations than reference formulation RM2 (RF microballoon) both in fed and fasted states in rabbits. The mean AUC(0-24) estimate of RCM3 was 55% higher in fasted state (p < 0.01) and about 51% higher in fed state (p < 0.05) relative to mean AUC(0-24) from RM2 formulation. Conclusively, enhancement in RF in the presence of CA along the entire plasma level curve suggests a possibility of reduction in dosing frequency. This controlled release drug delivery system of RF, where CA is incorporated in the microballoons can be easily encapsulated in capsule dosage form negating the need of CA solution as vehicle for administration of RF microballoons.