Nanostructured silicon oxides (SiOx) are close-to-market anode materials for increasing the energy density of next-generation lithium-ion batteries (LIBs), offering a balance between high capacity and enhanced cycling stability. However, achieving precise control over SiOx composition while maintaining structural integrity remains a challenge. In this study, we pioneer the use of nanostructured diatom-SiO2 frustules from industrially cultured Nitzschia sp. microalgae as a sustainable and tunable precursor for high-performance SiOx anodes via scalable magnesiothermic reduction reaction (MgTR). By optimizing the Mg-to-diatom-SiO2 molar ratio, we demonstrate controlled partial reduction of SiO2, yielding Si nanocrystals embedded within an SiO2 matrix. Notably, we reveal that the preservation of diatom-SiOx nanoporosity is highly sensitive to reaction exothermic conditions and is effectively stabilized by introducing NaCl as a heat scavenger. Tailoring the reactant composition (SiO2:Mg:NaCl = 1:1:2.5) resulted in anodes with superior electrochemical performance, delivering high capacity retention over 200 cycles. Through a comprehensive suite of characterization techniques, we establish the structure-property-performance relationships governing SiOx anode behavior. These findings mark a major advancement in sustainable SiOx anode design, providing a scalable strategy for integrating biologically templated nanostructures into high-performance LIBs.