We investigate the quark deconfinement phase transition in the context of binary neutron star (BNS) mergers. We employ a new finite-temperature composition-dependent equation of state (EOS) with a first order phase transition between hadrons and deconfined quarks to perform numerical relativity simulations of BNS mergers. The softening of the EOS due to the phase transition causes the merger remnants to be more compact and to collapse to a black hole (BH) at earlier times. The phase transition is imprinted on the postmerger gravitational wave (GW) signal duration, amplitude, and peak frequency. However, this imprint is only detectable for binaries with sufficiently long-lived remnants. Moreover, the phase transition does not result in significant deviations from quasi-universal relations for the postmerger GW peak frequency. We also study the impact of the phase transition on dynamical ejecta, remnant accretion disk masses, r-process nucleosynthetic yields and associated electromagnetic (EM) counterparts. While there are differences in the EM counterparts and nucleosynthesis yields between the purely hadronic models and the models with phase transitions, these can be primarily ascribed to the difference in remnant collapse time between the two. An exception is the non-thermal afterglow caused by the interaction of the fastest component of the dynamical ejecta and the interstellar medium, which is systematically boosted in the binaries with phase transition as a consequence of the more violent merger they experience.