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The simultaneous switching activity in digital circuits challenges the design of mixed-signal SoCs. Rather than focusing on time-domain noise voltage minimization, this work optimizes switching noise in the frequency domain. A two-tier solution based on the on-chip clock scheduling is proposed. First, to cope with the switching noise at the fundamental clock frequency, which usually dominates in terms of noise power, a two-phase clocking scheme is employed for system timing. Second, on-chip clock latencies are manipulated to target harmonic peaks in specific frequency bands for the spectral noise optimization. An automated design flow, which allows for noise optimization in user-defined application-specific frequency bands, is developed. The effectiveness of our design solution is validated by measurements of substrate noise and conductive EMI (electromagnetic interference) noise on a test chip, which consists of four wireless sensor node baseband processors each addressing a distinct clock-tree-synthesis strategy. Compared to the reference synchronous design, the proposed clock scheduling solution substantially reduces noise in the target GSM-850 band, i.e., by 11.1 dB on the substrate noise and 12.9 dB on the EMI noise, along with dramatic noise peak drops measured at the 50-MHz clock frequency.