Organ morphogenesis depends on mechanical interactions between cells and tissues. These interactions generate forces that can be sensed by cells and affect key cellular processes. However, how mechanical forces contribute, together with biochemical signals, to the shaping of complex organs is still unclear. We address this question using the seed of Arabidopsis as a model system. We show that seeds first experience a phase of high anisotropic growth that is dependent on the response of cortical microtubule (CMT) to forces, which guide cellulose deposition according to shape-driven stresses in the outermost layer of the seed coat. However, at later stages of development, we show that seed growth is isotropic and depend on the properties of an inner layer of the seed coat that stiffens its walls in response to tension but has isotropic material properties. Finally, we show that the transition from anisotropic to isotropic growth is due to dampening of CMT responses to shape-driven stresses. Altogether, our work supports that spatiotemporally distinct mechanical responses control the shape of developing seeds in Arabidopsis .