We construct a tropical analogue of the Poincaré bundle and prove a (cohomological) Fourier-Mukai transform for real tori with integral structures. We then prove a tropical analogue of Beauville's generalized Poincaré formula for polarized abelian varieties. Some consequences include a geometric Riemann-Roch theorem for tropical abelian varieties, as well as a tropical Poincaré-Prym formula which was recently conjectured by Röhrle and Zakharov.