Pore-filling and carbonate-replacing silica is exceedingly common in carbonates, but the fundamental geochemical mechanisms that drive these silicification reactions during diagenesis remain poorly understood. An existing model has proposed that carbonate silicification proceeds through an interface-coupled dissolution-precipitation reaction, but it lacks a mechanism that enables pore fluids to reach the requisite level of supersaturation with respect to silica to allow nucleation and growth. Here, we present a sequence of batch experiments ranging in duration from 7 to 49 days designed to test the hypothesis that these reactions are facilitated by the formation and destruction of organo-silica complexes during diagenesis. Our results illustrate that the stability of organo-silica complexes is dependent upon the concentration of organic molecules in solution, as well as pH, salinity, and solution redox state. Together, these results allow us to present the following scheme for organo-silica complex mediation of silicification reactions: Firstly, the breakdown of organic matter in the presence of siliceous material creates organo-silica complexes, leading to silica-enriched pore fluids, a process which is enhanced by the anoxic conditions accompanying sediment burial. Then, as environmental conditions evolve (fO2, salinity, light, fCO2, pH…), the stability of the organo-silica complexes diminishes, and the organo-silica complexes break down. Simultaneously, the pore fluids become intensely silica-supersaturated, in direct proportion to the amount of organic material remaining in solution. The resulting supersaturation drives carbonate silicification via the precipitation of silica minerals, a process which is aided by the presence of silica “nuclei” (such as sponge spicules). This study contributes new data and a conceptual model that will aid in the ongoing quest to understand carbonate silicification reactions and their potential applications in hydrocarbon exploitation and geologic CO2 storage. Moreover, it helps to explain the common association between silica precipitates and organic mineral in the sedimentary rock record.