  We introduce the CP violating scalar leptoquark $S_3$ to explain the measured
values of the lepton universality ratios $R_{K^{(*)}}$. We derive constraints
on the CP-even and CP-odd components of the leptoquark Yukawa couplings
stemming from effects in $b \to s \mu \mu$ and $B_s$ mixing. For the $b \to s
\mu \mu$ processes we impose $R_{K^{(*)}}$, $\mathcal{B}(B_s \to \mu^+ \mu^-)$,
as well as CP-sensitive angular asymmetries $A_{7,8,9}$, whereas in the $B_s$
mixing sector $\Delta M_s$ and $S_{\psi\phi}$ are considered. Combining the
constraints within the $S_3$ model reveals that a large CP phase with a
definite sign is perfectly viable for a leptoquark of mass below a few TeV. For
larger mass of the $S_3$ leptoquark the CP phase is suppressed due to the
observables pertaining to the $B_s$ system. We provide predictions of direct
and mixing-induced CP asymmetries in $B \to K \mu \mu$ that could reveal the
presence of the novel CP phase.
