The seed oil of Carapa guianensis, known as crabwood oil (CWO), is distinguished for its medicinal and cosmetics applications, attributed to its bioactive components and lipid profile. CWO and its dry and solvent fractionation were studied, with a focus on physicochemical functionality and the partitioning of known bioactive compounds, such as limonoids and sterols. Important bioactive components, including limonoids and sterols, were partitioned depending on the fractionation method; in particular, there is a direct dependence on solvent polarity. There was a very strong solid fraction yield−solvent polarity with a high linear slope of −121.3%. The partitioning of the lipids is significant enough to drive measurable and predictable changes in the physical properties. Palmitic (P: C16:0) and oleic (O: C18:1) fatty acids account for about 60% of the total fatty acid composition of the TAGs of CWO and its fractions. The most abundant limonoid is methyl angolensate (from 28 to 39%), followed by Trichilin A (from 13% to 22%). Gedunin and Andirobin were more abundant in the liquid fractions, whereas Carapanolides (less than 1.3%) were more present in the olein fractions. The crystallization and melting temperatures of the solid fractions were up to 26 °C, compared to 11°C for CWO, and were particularly strongly correlated to the polarity of the solvents. The SFC profile indicated semi-solid fats, with the solid fractions showing up to 19% at 18 °C, twice the SFC in CWO. The fractions demonstrated a wide range of distinguishable microstructures. The shapes include well-organized spherulites and needle-like and rod-like crystals with sizes varying from 5 to 250 µ, suggesting that they are likely to have different flow characteristics and feel to the skin and mouth. There is a potential to make unique compositions with significantly different properties, with antimicrobial and antifungal efficacy due to the bioactive components of CWO through fractionation, using polarity as a predictive tool.