Abstract: We investigate the time evolution of spherically symmetric boson stars in Palatini f(R) gravity through numerical relativity computations. Employing a novel approach that establishes a correspondence between modified gravity with scalar matter and general relativity with modified scalar matter, we are able to use the techniques of numerical relativity to simulate these systems. Specifically, we focus on the quadratic theory f(R) = R + xi R2 and compare the obtained solutions with those in general relativity, exploring both positive and negative values of the coupling parameter xi. Our findings reveal that boson stars in Palatini f(R) gravity exhibit both stable and unstable evolutions. The latter give rise to three distinct scenarios: migration toward a stable configuration, complete dispersion, and gravitational collapse leading to the formation of a baby universe structure.