A number of studies have shown that Fourier transform infrared spectroscopy (FTIRS) can be applied to quantitatively assess lacustrine sediment constituents. In this study, we developed calibration models based on FTIRS for the quantitative determination of biogenic silica (BSi; n=420; gradient: 0.9–56.5%), total organic carbon (TOC; n = 309; gradient: 0–2.9 %), and total inorganic carbon (TIC; n = 152; gradient: 0–0.4 %) in a 318 m-long sediment record with a basal age of 3.6 million years from Lake El’gygytgyn, Far East Russian Arctic. The developed partial least squares (PLS) regression models yield high cross-validated (CV) RC2V=0.86–0.91andlowrootmeansquareerrorofcross- validation (RMSECV) (3.1–7.0 % of the gradient for the dif- ferent properties). By applying these models to 6771 sam- ples from the entire sediment record, we obtained detailed insight into bioproductivity variations in Lake El’gygytgyn throughout the middle to late Pliocene and Quaternary. High accumulation rates of BSi indicate a productivity maximum during the middle Pliocene (3.6–3.3 Ma), followed by grad- ually decreasing rates during the late Pliocene and Qua- ternary. The average BSi accumulation during the middle Pliocene was ⇠ 3 times higher than maximum accumulation rates during the past 1.5 million years. The indicated progres- sive deterioration of environmental and climatic conditions in the Siberian Arctic starting at ca. 3.3 Ma is consistent with the first occurrence of glacial periods and the finally com- plete establishment of glacial–interglacial cycles during the Quaternary.