We evaluated the fatty acid compositions in relation to yield and soil nutrients from four fields A, B, C, and D with continuous monocropping histories of 0–3 years, respectively, in Japan from 2015 to 2016. Results showed that, in both evaluation years, seed yield did not significantly differ among the fields although field A produced the highest mean seed yield and 1000-seed weight. Between fields A and C, 1000-seed weight showed significant differences. The contents of seed-saturated fatty acids lauric and myristic decreased in only fields C and D whereas oleic, linoleic, and linolenic acids increased in field D. Only field A produced the highest contents of lauric and myristic acids whereas field D produced the highest contents of linoleic and linolenic acids. The soil total N and exchangeable K contents tended to decrease as exchangeable Mg content significantly increased on the fields with long duration of cropping, fields C and D. Principal component analysis revealed significant positive correlations between soil exchangeable K, and total N contents with 1000-seed weight and lauric acid, as exchangeable Mg content was related with oleic, linoleic, and linolenic acids. Therefore, the high oleic, linoleic, and linolenic acids from field D were mainly attributed to high soil exchangeable Mg content, whereas the high 1000-seed weight, lauric acid and myristic acid were due to the high soil exchangeable K content in field A. Overall, the fatty acid composition quality on the long-duration continuously monocropped fields could show high economic value at the expense of yield under this management practice in continuous monocropping.