Alkyd resins are oil-based polymers that have been widely used for generations in the surface coating industry and beyond. Characterization of these resins is of high importance to understand the influence of its components on its behavior, compatibility with other resins, and final quality to ensure high durability. Here, NMR spectroscopy and GPC were used for characterizing differences in the chemical structure, molecular distribution, and dispersity between oil-based and fatty acid-based alkyd polymers made from sacha inchi and linseed oils. Sancha inchi (Plukentia volubilis L.) is a fruit-bearing plant native to South America and the Caribbean, and has a rich unsaturated fatty acid content. The effect of vegetable oil and polyol selection on the synthesis of alkyd resins for coating applications was analyzed. The influence of two different synthesis methods, monoglyceride and fatty acid processes, was also compared. Important structural differences were observed using NMR: one-dimensional spectra revealed the degree of unsaturated fatty acid chains along the polyester backbone, whereas, 2D NMR experiments facilitated chemical shift assignments of all signals. GPC analysis suggested that alkyd resins with homogeneous and high molecular weights can be obtained with the fatty acid process, and that resins containing pentaerythritol may have uniform chain lengths.