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We introduce the CP violating scalar leptoquark S3 to explain the measured values of the lepton universality ratios RK(∗). We derive constraints on the CP-even and CP-odd components of the leptoquark Yukawa couplings stemming from effects in b → sμμ and Bs mixing. For the b → sμμ processes we impose RK(∗), B(Bs → μ+μ−), as well as CP-sensitive angular asymmetries A7,8,9, whereas in the Bs mixing sector ∆Ms and Sψφ are considered. Combining the constraints within the S3 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 S3 leptoquark the CP phase is suppressed due to the observables pertaining to the Bs system. We provide predictions of direct and mixing-induced CP asymmetries in B → Kμμ that could reveal the presence of the novel CP phase.