Short periods of multitude abiotic stresses are expressed in soybean throughout the growing season. Some of them exhibit a long-term impact on the crop performance affecting the yield in soybean. Environmental stress exhibits a high degree of selectivity in the accumulation of proteins during seed development. There was a 40% reduction in glycinin level while that of β-conglycinin was elevated under sulfur deficiency in the developing seeds of soybean. The soybean plants exhibit physiological responses under nutrient deficiencies some of which might be associated with nutrient-use efficiency (NUE) changes of nitrogen and phosphorus. An improvement in understanding of the biological processes and genes involved in conferring stress tolerance so as to mitigate the seasonal yield loss likely to occur at the end have indicated that soybean crop exhibits transcriptional response when exposed to sequential or repeated nutrient stresses. These responses vary in accordance with conditions that prevail at the field level during the growth period. A core group of genes is preserved despite repeated stress exposures to these nutrients, according to the transcriptional profile of soybean plants treated to iron deficit followed by phosphate deficiency stress. The transcriptional responses are particularly noticeable with genes involved in reproduction, which is one of the transcriptome’s plasticity responses to successive nutritional stress exposures in soybeans.