Fortification of foods with L-5-methyltetrahydrofolic acid (L-5-MTHF) is challenging due to low stability to environmental conditions that include exposure to pH, moisture, and temperature. The objective of the present study was to stabilize L-5-MTHF using microencapsulation technology. L-5-MTHF microcapsules constructed with different core-to-wall ratios of L-5-MTHF, both alone or in combination with sodium ascorbate, yielded high (>89%) recovery of L-5-MTHF. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis confirmed successful encapsulation of L-5-MTHF with high core-to-wall ratios. Microencapsulation of L-5-MTHF alone with a high core-to-wall ratio significantly (p < 0.05) improved the stability of L-5-MTHF over the course of bread baking, performed both in pilot plant and in commercial baking conditions. Breads made with fortified flour containing sodium ascorbate coencapsulated with L-5-MTHF had recoveries of L-5-MTHF that were 97% and 77%, respectively, for pilot plant and bakery breads. Co-encapsulating L-5-MTHF with ascorbate also significantly (p < 0.05) improved stability during storage, as compared to breads that contained free L-5-MTHF.