This paper focuses on the study of the contents of inkwells dating to the Early Roman period, using an array of analytical techniques: portable X-ray fluorescence spectrometer (pXRF), Raman spectroscopy, powder X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy combined with energy dispersive X-ray spectroscopy (SEM-EDS). Our goal was to shed light on the chemical composition of the inks used for writing in the late Second Temple period in Israel, particularly those which may have been similar to that used in the Dead Sea Scrolls (DSS). An understanding of the ancient ink’s chemistry has important implications for conservation and preservation purposes, and may reveal important information about ancient scribal practices and writing schools. Although most of the analyzed inkwells revealed no ink residues, molecular traces of bone-derived carbon were detected in one sample, plausibly originating from bone black pigment used in ancient ink. Organic residues from three other inkwells may be the remains of ink binders.