The oceans hold a large amount of refractory dissolved organic carbon (RDOC) that plays an important role in carbon sequestration and climate regulation. Previous bioassay experiments have demonstrated a rapid and efficient microbial production of complex molecules from simple substrates, a process contributing to the formation of RDOC in the ocean. However, early measurements of biomarkers indicated only ~25% of the marine DOC is derived from bacteria, leading to an uncertainty about the fate of the RDOC continuously produced by bacteria in the ocean. To address this question, we conducted time-series bioassay experiments using natural microbial communities inoculated into carbon‑free artificial seawater. Labile organic substrates were added every 2-4 months to stimulate repeated production of bacterial molecules over a two-year period. We analyzed amino acid compounds to provide molecular insight into the fate of bacterially-derived RDOC. Our results revealed that microorganisms rapidly consumed the labile substrates, producing new and persistent molecules that accounted for <5% of the initial carbon. With each subsequent cycle, concentrations of bacterially-derived DOC increased, although the efficiency of accumulation varied across cycles. Molecular analysis of amino acids showed a similar accumulation pattern, while individual amino acids exhibited diverse fates. These findings suggest that microbially-derived molecules follow different pathways and together lead to an overall accumulation of bulk DOC. However, the extent of this accumulation appears to be influenced by various factors and processes.