The Green Deal targets, along with tightening emissions legislation, foster research on alternative propulsion systems. In non-road mobile machinery (NRMM), these efforts largely rally around sustainable fuels while keeping the benefits of energy security (multi-fueling) high. In this context, the blends of Hydrogenated Vegetable Oil (HVO) and Methanol (MEOH) are amongst the most promising yet under-researched alternatives and, as such, need dedicated methods for determining their suitability in engine applications. In this paper, we evaluate the feasibility of Fourier transform infrared (FTIR) analytics for determining the stability of MEOH-HVO mixtures. The research considers temperature effects during storage by conditioning the test samples at −20 °C and +20 °C. The stability of the blends and different co-solvents is analysed after six weeks, and FTIR spectra are used to identify the chemical bonds. From FTIR analysis, blending MEOH20 with 1-dodecanol results in stable homogenous alkyl-ether fuels, while the MEOH20 blend with methyl-butyrate results in ester fuels. There are observable differences in the blend samples according to their storage temperatures. In conclusion, both fuel blend samples formed different fuel types, which are stable and homogenous at room temperature, posing great potential for their applicability in different NRMM types.