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Soybean (Glycine max (L.) Merrill) is an important source of oil for biodiesel production in Brazil. However, the traits related to oil content and fatty acid profile are not targeted by soybean breeding programs. Developing methods to increase oleic and reduce linolenic fatty acid content within soybean genotypes will increase the use of soybeans for food and feed, as well as biodiesel production. Biodiesel produced with high polyunsaturated fatty acids (PUFAs) content has a high tendency to undergo oxidation, making storage difficult and overall quality reduced. On the other hand, oils with high levels of monounsaturated fatty acids (MUFAs) are preferred for biodiesel production because oxidation is not increased, improve cold flow properties significantly and nitrogen oxide emissions are decreased. In addition, soybean oil with high concentration of PUFAs causes low oxidative stability, resulting in rancidity, a rapid decline of optimal flavor and reducing storage time of manufactured food products. 242 recombinant inbred lines (RILs) were evaluated in six locations in Brazil for grain yield, oil content, oil production, and fatty acid composition. A multi-trait index based on factor analysis and ideotype-design (FAI-BLUP index) was applied to identify genotypes best related with the ideotype for biodiesel production. This method is based on mixed models, with genotype and environment effects being considered as random and fixed, respectively. In addition, the best linear unbiased prediction (BLUP) method was used to predict the genetic values. Six RILs outperformed both parents and can be selected as genotypes more suitable for biodiesel production. Genetic selection reduced linolenic fatty acid content by 14%. Results indicated the presence of genetic variability for fatty acid composition. The significant increases in oleic and reductions in linolenic contents may be easily achieved with the introduction of mutant FAD2-1A and FAD2-1B genes through breeding programs or biotechnological strategies.