To better understand the recent internal structure of Misti volcano, we determined a 3D S-wave velocity model applying Ambient Noise Tomography (ANT). We used data from 23 broadband and short-period seismic stations temporarily installed at Misti volcano between March and December 2011. This dataset allowed us to obtain empirical Green's functions by cross-correlating seismic ambient noise signals. Then, we retrieved 104 dispersion curves using the frequency-time analysis (FTAN) and, through a non-linear multiscale inversion, we obtained nine 2-D Rayleigh waves group velocity maps for periods in the range 0.7 s - 2 s. Finally, we carried out the depth inversion through a Bayesian transdimensional inversion to obtain a 3-D S-wave velocity model down to 3 km depth. Our study highlights five relevant seismic velocity anomalies. We observed the presence of three high-velocity zones located in the west-northwest, southwest and southeast parts of the crater, that could be related to intrusive bodies possibly associated with the formation of Misti volcano. We also observed two low-velocity anomalies in the volcano's western and central parts, which coincide with previous studies' findings and are related to fractured and weakened materials associated with the external caldera collapse and recent eruption episodes.