The bioenergy crops such as energycane, miscanthus, and sorghum are being genetically modified using state of the art synthetic biotechnology techniques to accumulate energy-rich molecules such as triacylglycerides (TAGs) in their vegetative cells to enhance their utility for biofuel production. During the initial genetic developmental phase, many hundreds of transgenic phenotypes are produced. The efficiency of the production pipeline requires early and minimally destructive determination of oil content in individuals. Current screening methods require time-intensive sample preparation and extraction with chemical solvents for each plant tissue. A rapid screen will also be needed for developing industrial extraction as these crops become available. In the present study, we have devised a proton relaxation nuclear magnetic resonance (¹H-NMR) method for single-step, non-invasive, and chemical-free characterization of in-situ lipids in untreated and pretreated lignocellulosic biomass. The systematic evaluation of NMR relaxation time distribution provided insight into the proton environment associated with the lipids in the biomass. It resolved two distinct lipid-associated subpopulations of proton nuclei that characterize total in-situ lipids into bound and free oil based on their “molecular tumbling” rate. The T1T2 correlation spectra also facilitated the resolution of the influence of various pretreatment procedures on the chemical composition of molecular and local ¹H population in each sample. Furthermore, we show that hydrothermally pretreated biomass is suitable for direct NMR analysis unlike dilute acid and alkaline pretreated biomass which needs an additional step for neutralization.