Trade-offs between growth and reproduction in soybean require resource availability manipulations. Decapitation and reducing sink strength through deflowering can affect the source–sink ratio that affects plant growth, development, and yield. The current study assesses the effect of decapitation (Decap) and removal of the two lowest racemes (R2LR) and their combination on growth, flowering, and yield capacity of soybean through controlling the source–sink ratio and inducing the “stay-green” phenotype. Two field experiments were conducted during 2018 and 2019 in the Agronomy Farm located at Mansoura University, Egypt. Decapitation was done at the V4 stage (35 days after sowing, DAS), during which four nodes on the main stem had fully developed leaves beginning with the unifoliolate nodes, whereas R2LR was performed at the R2 stage (50 DAS), during which the plants had one open flower at one of the two uppermost nodes on the main stem. Results indicated that Decap, R2LR, and their combination significantly increased seed yield per plant through increasing plant growth and flowering and improving biochemical attributes. The combination between Decap and R2LR was generally more effective in positively modulating plant vegetative, reproductive, and physiological capacity than either Decap or R2LR alone. Moreover, the number of branches as well as pods/plant and IAA content responded positively to Decap, whereas net assimilation rate, seed growth rate, number of flowers/node, and cytokinins content responded positively to R2LR. Decap and R2LR were interpreted in light of their effects on inducing the “stay-green” phenotype and altering the source–sink ratio. Based on the findings, it can be concluded that concealing the apical dominance in conjunction with reducing the sink strength through guided raceme removal would be beneficial for the reproductive potential in soybean.