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The kinetics of phase transitions during formation of small-scale systems are essential for many applications. However, their experimental observation remains challenging, making it difficult to elucidate the underlying fundamental mechanisms. Here, we combine in situ and real-time synchrotron X-ray diffraction (XRD) and X-ray reflectivity (XRR) experiments with substrate curvature measurements during deposition of nanoscale Mo and Mo 1-x Si x films on amorphous Si (a-Si). The simultaneous measurements provide direct evidence of a spontaneous, thickness-dependent amorphous-to-crystalline (a-c) phase transition, associated with tensile stress build-up and surface roughening. This phase transformation is thermodynamically driven, the metastable amorphous layer being initially stabilized by the contributions of surface and interface energies. A quantitative analysis of the XRD data, complemented by simulations of the transformation kinetics, unveils an interface-controlled crystallization process. This a-c phase transition is also dominating the stress evolution. While stress build-up can significantly limit the performance of devices based on nanostructures and thin films, it can also trigger the formation of these structures. The simultaneous in situ access to the stress signal itself, and to its microstructural origins during structure formation, opens new design routes for tailoring nanoscale devices.