The food industry has been expanding, and new vectors to entrap vitamins have been constantly investigated, aiming at versatile systems with good physico-chemical characteristics, low-cost production, high stability and the efficient release of active ingredients. The vitamin B9 (folic acid or folate) is essential for the healthy functioning of a variety of physiological processes in humans and is beneficial in preventing a range of disorders. In this study, two approaches were developed to encapsulate vitamin B9. Zein and the combination of modified starch with two plasticizers were the selected encapsulating agents to produce microstructures via the electrospinning technique. The objective was to improve the stability and the B9 antioxidant capacity in the final formulations. The work strategy was to avoid limitations such as low bioavailability, stability and thermosensitivity. The microstructures were fabricated and the morphology and shape were assessed by scanning electron microscopy. The B9 release profiles of modified starch and zein microstructures were analyzed in simulated gastric fluid at 37 °C, and in deionized water and ethanol at room temperature. The B9 encapsulation efficiency and the stability of the systems were also studied. The ABTS assay was assessed and the antioxidant activity of the produced microstructures was evaluated. The physico-chemical characterization of loaded B9 in the microstructures was achieved. High encapsulation efficiency values were achieved for the 1% B9 loaded in 12% w/w modified starch film; 5% B9 vitamin encapsulated by the 15% w/w modified starch with 4% w/w tween 80; and 4% w/w glycerol film with heterogeneous microstructures, 5% w/w zein compact film and 10% w/w zein film. In conclusion, the combinations of 7 wt.% of modified starch with 4 wt.% tween 80 and 4 wt.% glycerol; 15 wt.% of modified starch with 4 wt.% tween 80 and 4 wt.% glycerol; and 12 wt.% modified starch and 5 wt.% zein can be used as delivery structures in order to enhance the vitamin B9 antioxidant activity in the food and nutraceutical fields.