In laboratory experiments on field-collected sediments, we investigated 7.8 million-year-old sediment from a site off the Nankai Trough, Japan, through incubation experiments to simulate future burial conditions. In a 55-day laboratory experiment, we incubated sediment slurried with artificial seawater in four subsets at 20°C (control), and at 35°C, 55°C, and 85°C to simulate future heating during burial and conditions favorable for mesophilic, thermophilic, and hyperthermophilic microorganisms, respectively. We investigated changes in dissolved organic matter quality as a function of microbial activity and temperature using 3D fluorescence spectroscopy (EEMs) and FT-ICR-MS, and analyzed dissolved manganese, iron, and sulfur to detect changes in the sediment's mineral matrix. We observed temperature- and time-dependent changes in the dissolved organic matter (DOM) pool. Data contains (1) bulk parameters about organics and inorganics in the dissolved phase, (2) release of the acetate during laboratory experiments, (3) details about the formulae characterized by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS).