This study investigated long-term agronomic management systems and precipitation level effects on soybean [Glycine max (L.) Merr.] total oil content and fatty acid composition. Management systems evaluated included conventional (CT), no-till (NT), low chemical input (LI), and zero chemical input (ORG). Total oil content and major fatty acids profiles were analyzed by accelerated solvent extractor (ASE 200) and gas chromatography with flame ionization detector (FID). The results showed these four management systems have limited influence on soybean grain total oil content and oleic acid (O) and linoleic acid (L) compositions. The NT management system significantly improved soybean oil yield on a land-area basis as a result of higher annual grain yields. Soybeans grown under the NT management system had as high or higher palmitic acid (P) composition than the other three management systems; similarly, the CT treatments had as low or lower linolenic acid (LN) composition in soybean when compared with the other three management systems. The levels of stearic acid (S), O, L, and LN had a significant quadratic relationship (R2 = 0.64–0.75) with total (July–September) precipitation. The oil quality ratio of O/(L + LN) had a quadratic relation with precipitation.