Vitamins, exogenous organic compounds that play a vital role in metabolic reactions, and fundamental powerful antioxidants with a crucial role in the genetic transcription process, are considered essential nutritional factors. Folic acid (FA), also known as folate, or Vitamin B9, plays an indispensable role in various intracellular reactions, being the main pawn, with a strong impact on medical and dental science. The aim of this paper mainly focuses on presenting the latest and most advanced aspects related to the following topics: (1) the resonance that FA, and more specifically FA deficiency, has at the level of the oral cavity; (2) the elements involved in the molecular landscape, which reflect the interaction and the possible mechanisms of action, through which FA influences oral health; and (3) the particular processes by which FA deficiency causes certain clinical conditions. Moreover, we aim to draw the attention and trigger the curiosity of health professionals on the need to know the specific host–environment interactions, particularly the linkage between individual genotype and phenotypic variability, which in the future could represent the basis of novel and effective treatment methods. From this perspective, we begin by providing an overview of the general radar echo of the human body induced by FA deficiency, before focusing on the genetic strategic substrate and biochemical processes involved in the molecular mechanisms through which FA acts at the cellular level. Finally, we reflect on the resulting conclusions: (1) the complex interrelationships between different types of cytokines (CKs) and abnormal folate metabolism are involved in the occurrence of neural tube defects (NTDs) and orofacial clefts (OFCs); (2) increased oxidative stress, endothelial dysfunction, and genomic instability, induced by folate deficiency, have a major impact on periodontal health; and (3) glutamate carboxypeptidase II, GCP2 1561C>T allelic variant, constitutes the main pawn, which specifically influences the bioavailability of natural folates and FA, as the main actors, with essential roles in oral health.