Seed is the dissemination unit of plants initiating an important stage in the life cycle of plants. Seed development, comprising two phases: embryogenesis and seed maturation, may define the quality of sown seed, especially under abiotic stress. In this review we have focused on the recent advances in the molecular mechanisms underlying these complex processes and how they are controlled by distinct environmental factors regulating ion homeostasis into the seed tissues. The role of transporters affecting seed embryogenesis and first stages of germination as imbibition and subsequent radicle protrusion and extension were revised from a molecular point of view. Seed formation depends on the loading of nutrients from the maternal seed coat to the filial endosperm, a process of which the efflux is not clear and where different ions and transporters are involved. The clear interrelation between soil nutrients, presence of heavy metals and the ion capacity of penetration through the seed are discussed in terms of ion effect during different germination stages. Results concerning seed priming techniques used in the improvement of seed vigor and radicle emergence are shown, where the use of nutrients as a novel way of osmopriming to alleviate abiotic stress effects and improve seedlings yield is discussed. Novel approaches to know the re-translocation from source leaves to developing seeds are considered, as an essential mechanism to understand the biofortification process of certain grains in order to cope with nutrient deficiencies, especially in arid and semiarid areas. Finally, the role of new genes involved in hormone-dependent processes, oxidative response and water uptake into the seeds during their development or germination, have been described as plant mechanisms to deal with abiotic stresses.