Mass spectrometry ranks as the predominant method for molecular lipidomic analysis, spanning health, food and manufacturing industries. However, orthogonal methods to validate, optimise, and assess quality and quantity of lipid samples are scarce. Here, we investigate attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy as a rapid method for lipid sample quality control and absolute quantitation. Through analysis of vibrational frequencies, FTIR spectroscopy can monitor all classes of biomolecules in a single analysis. We demonstrate the application of FTIR to detect common lipid sample contaminants, such as water, sugars, and protein, using a small volume of mass spectrometry-compatible sample. To enable quantitation, several commercially available lipid standards were evaluated for standard curve generation and to determine detection limits. Finally, the accuracy of FTIR-based lipid quantitation was evaluated through parallel ATR-FTIR and mass spectrometry (dynamic multiple reaction monitoring) in human plasma samples (n = 105). In summary, we report a novel, mass spectrometry-compatible method for rapid (~5-10 min) lipid quantitation and quality control using minimal sample (1-3µL, typically less than 1/30th of the sample), which would be useful in lipidomics research.