The essentiality of selenium (Se) and iodine (I) for the human organism and the relationship between these two trace elements in mammal metabolism highlight the importance of the joint Se–I biofortification to vegetable crops in the frame of sustainable farming management. A research study was carried out in southern Italy to determine the effects of the combined inoculation with arbuscular mycorrhizal fungi (AMF) and biofortification with Se and I on plant growth, seed yield, quality, and antioxidant and elemental status, as well as residual biomass chemical composition of chickpea grown in two different planting times (14 January and 28 February). The AMF application improved the intensity of I and Se accumulation both in single and joint supply of these elements, resulting in higher seed yield and number as well as dry weight, and was also beneficial for increasing the content of antioxidants, protein, and macro- and microelements. Earlier planting time resulted in higher values of seed yield, as well as Se, I, N, P, Ca, protein, and antioxidant levels. Se and I showed a synergistic effect, stimulating the accumulation of each other in chickpea seeds. The AMF inoculation elicited a higher protein and cellulose synthesis, as well as glucose production in the residual biomass, compared to the single iodine application and the untreated control. From the present research, it can be inferred that the plant biostimulation through the soil inoculation with AMF and the biofortification with Se and I, applied singly or jointly, proved to be effective sustainable farming tools for improving the chickpea seed yield and/or quality, as well as the residual biomass chemical composition for energy production or beneficial metabolite extraction.