We present the results on CP-violation searches in the $B_s$ system, studied in the $B_s\rightarrow J/\psi \phi$ decay, and in the $B_d$ system through the comparison of the decay time distributions in the flavour specific state $J/\psi\ K^*$ and in the CP eigenstate $J/\psi\ K_s$. We also present new results in the search for the rare decays of $B_d$ and $B_s$ into $\mu^+\mu^-$. All results are based on the full sample of $pp$ collisions data recorded during LHC Run 1 by the ATLAS detector at $\sqrt{s}$ 7 and 8 TeV. The consistency with the Standard Model predictions and with other available measurements is discussed.