Quantifying light elements such as carbon, nitrogen, and oxygen in a transmission electron microscope (TEM) is a challenging however essential task in biology, materials, or earth and planetary sciences. We have developed an approach that allows precise quantification by energy-dispersive X-ray spectroscopy (EDXS), using sensitive windowless silicon drift detectors and homemade Python routines for hyperspectral data processing. K-factors were determined using wedge-shaped focused ion beam sections. To correct for X-ray absorption within the sample, the sample mass thickness is determined by the—revisited—two-lines method (Morris, 1980). No beam current measurement is required. Applying this method to the K and L lines of iron, we found that the tabulated mass absorption coefficient at the energy of the iron L lines was too low. This is due to X-ray self-absorption at the iron edge. Using reference material, we experimentally determined an absorption coefficient that gave the expected results. We then analyzed the complex phyllosilicate mixture of the Orgueil meteorite. We show that the N/C ratio of organics can be obtained with an accuracy better than 5 at.% and that oxygen can be quantified accurately enough to infer the hydroxyl content of phyllosilicates.