We investigated experimentally and numerically the spectral control of modulation instability (MI) dynamics via the initial phase relation of two weak seed fields. Specifically, we show how second-order modulation instability dynamics exhibit phase-dependent anticorrelated growth rates of adjacent spectral sidebands. This effect enables a novel method to control MI-based frequency conversion: in contrast to first-order MI dynamics, which exhibit a uniform phase dependence of the growth rates, second-order MI dynamics allow to redistribute the spectral energy, leading to an asymmetric spectrum. Therefore, the presented findings should be very attractive to different applications, such as phasesensitive amplification or supercontinuum generation initiated by MI.