Inositols are a class of biologically active compounds which can be used as precursors for the synthesis of a wide range of bioactive products. Lately, there is growing awareness on the importance of developing chiral compounds in the pharmaceutical and nutraceutical industries. This new emphasis on chiral compounds boils down to safety matters, with an aim to select the right enantiomer for desired biological activities. Natural rubber serum (NRS) has the advantage as it possesses a significant percentage of naturally occurring bioactive inositol compounds. For this study, considerable amounts of quebrachitol (2-O-methyl-L-chiro-inositol) were isolated from NRS using membrane separation technology and converted to L-chiro-inositol crystals. Characterisations of the resulting inositol compounds were performed using Fourier transform infrared spectroscopy (FTIR), high-performance liquid chromatography–mass spectrometry (LCMS) and liquid-state nuclear magnetic resonance (NMR) spectroscopy methods. FTIR and NMR results for the L-chiro-inositol compound obtained showed similar spectrums as the commercial control, while LCMS mass spectra was demonstrated to be at m/z 179.03 (M–H)− in the negative ionisation mode, confirming the compound to be L-chiro-inositol. Thus, it can be concluded that quebrachitol from NRS obtained via membrane separation technology and its modified inositol derivatives have high potential market value to be used as building blocks for pharmaceutical and nutraceutical applications. Quebrachitol already exists naturally as an enantiomer and chiral compound in the rubber tree, and instead of being treated as a waste product, its usage can actively contribute to tackling environmental pollution from rubber processing effluents.