Unrefined, refined and refined-deodorized cottonseed oils from pressing or extraction technologies were screened using proton (1H) nuclear magnetic resonance (NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS). GC–MS of derivarized and non-derivatized (intact oil) cottonseed oils allowed detection of nearly 100 compounds. These included fatty acids (FA), linoleic (relative percentage concentration of 51–58%), palmitic (21–24%), oleic (18–23%) and stearic acids (1.8–2.2%) in hydrolysed oils, and β-sitosterol (31–43%), linoleic acid (7–29%), γ- and α-tocopherol (11–22%), and squalene (2–4%) in intact oils. NMR spectra of intact oils contained 91 resonances and were dominated by methylene (40.7–41.4%), methyl (14.1–14.2%), and methine (6.7–6.8%) protons of FA and triglycerides. Analysis of the molecular profiles revealed a dominating effect of the processing followed by the production technology. Oil refinement reduced undesirable free FA, diglycerides and gossypol, but increased hydrocarbons and aldehydes. The refined press oil contained higher levels of steroids and less free FA compared to refined extract oil. Thus, the study showed the potential of foodomics to evaluate the in-depth molecular quality of edible oils.