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We consider a dark sector consisting of dark matter that is a Dirac fermion and a scalar mediator. This model has been extensively studied in the past. If the scalar couples to the dark matter in a parity conserving manner then dark matter annihilation to two mediators is dominated by the P-wave channel and hence is suppressed at very low momentum. The indirect detection constraint from the anisotropy of the Cosmic Microwave Background is usually thought to be absent in the model because of this suppression. In this letter we show that dark matter annihilation via bound state formation occurs through the S-wave and hence there is a constraint on the parameter space of the model from the Cosmic Microwave Background.