We present a detailed analysis based on both experimental and 3D modelling approaches of the unique silicon nitride precipitation sequence observed in ferritic Fe-Si alloys upon nitriding. At 570 °C, Si3N4 silicon nitride was shown to form as an amorphous phase into α-Fe ferrite matrix, which is morphologically unstable over time. Precipitates nucleated with a spheroidal shape, then developed a cuboidal shape for intermediate sizes and octapod-like morphology for a longer time. Using transmission electron microscopy, we show that the transition between spheroid and cuboid morphology depended on particle size and resulted from competition between interfacial energy and elastic strain energy. The resulting morphology was then shown to be a cuboid shape whose faces were always parallel to the {100} planes of the α-Fe; the <100> directions of the matrix corresponded to the elastically soft directions. There was a critical size of around 45 nm for which the transition between the cuboid shape and the octapod-like morphology took place. This was characterised by a transformation of quasi-flat facets into concave ones and the development of lobes in the <111> directions of the bcc crystal. To better assess the kinetic effects of diffusion fields and internal stresses on the morphological instability observed, an original 3D model that explicitly coupled phase transformations and mechanical fields was developed and applied. The latter, validated on the basis of model cases, was shown to be able to describe the time-evolution of both chemical and mechanical fields and their interactions in diffusive mass transport. Using a model system, it was shown that the concentration field around the precipitates and the internal stresses played opposing roles in the cuboid to octapod-like morphological instability. This work gives some clarification regarding the morphological evolution of amorphous Si3N4 precipitates, an important point for controlling the mechanical properties of nitrogen steels.