Waterborne polyurethanes (WBPU) based on the reaction of unmodified castor oil (CO) with isophorone diisocyanate (IPDI) were synthesized using dimethylolpropionic acid (DMPA) or tartaric acid (TA) as internal emulsifiers. The effect of the incorporation of TA, a bio-based carboxylic acid, in the synthesis of castor oil-based WBPU was carefully investigated. For comparison, two WBPUs were synthesized using DMPA. The chemical changes that took place during the reaction were followed using FTIR. The raw materials and the final polymeric films were characterized by this technique as well as 1HNMR, XRD, DSC, DMA and TGA. Results indicated that in the case of the sample prepared with TA, the isocyanate reacts with the hydroxyls of the acyl groups of the acid additionally to the alcoholic ones. In all cases, the films prepared by casting were translucent and showed glass transition temperatures above room temperature, although comparatively lower for the WBPU formulated with TA. Differences were also observed in the thermal degradation performance of the films. The observed differences were tracked to those in the molecular structures of the WBPUs.