Operando Raman spectroscopy and synchrotron X-ray diffraction were combined to probe the evolution of strain in Li-ion battery anodes made of crystalline silicon nanoparticles. The internal structure of the nanoparticles during two discharge/charge cycles was evaluated by analyzing the intensity and position of Si diffraction peaks and Raman TO-LO phonons. Lithiation/delithiation of the silicon under limited capacity conditions triggers the formation of "crystalline core-amorphous shell" particles, which we evidenced as a stepwise decrease in core size, as well as sequences of compressive/tensile strain due to the stress applied by the shell. In particular, we showed that different sequences occur in the first and the second cycle, due to different lithiation processes. We further evidenced critical experimental conditions for accurate operando Raman spectroscopy measurements due to the different heat conductivity of lithiated and delithiated Si. Values of the stress extracted from both operando XRD and Raman are in excellent agreement. Long-term ex situ measurements confirmed the continuous increase of the internal compressive strain, unfavorable to the Si lithiation and contributing to the capacity fading. Finally, a simple mechanical model was used to estimate the sub-nanometer thickness of the interfacial shell applying the stress on the crystalline core. Our complete operando diagnosis of the strain and stress in SiNPs provides both a detailed scenario of the mechanical consequences of lithiation/delithiation in SiNP and also experimental values that are much needed for the benchmarking of theoretical models and for the further rational design of SiNP-based electrodes.