Soybean [Glycine max (L.) Merr.] is a global protein source and is currently expanding in Central and Northern Europe. Protein and oil content are two important quality traits that have been studied in different germplasm, however, their genetic architecture in early-maturing European soybean has not been investigated yet. In this study, we therefore performed QTL mapping for both traits using 944 recombinant inbred lines derived from eight families from a half-diallel crossing design. We identified five QTL for each trait, with the QTL on chromosomes 8, 15, and 20 being identified for both protein content and oil content. The known major QTL on chromosome 20 was detected in four families whereas the other QTL were only found in single families. Further analyses revealed the QTL to have pleiotropic but inverse effects on both traits. The effect of the major QTL was comparable between families, illustrating that it is largely independent from the genetic background. Collectively, our results illustrate the quantitative nature of protein and oil content in early European soybean. Marker-assisted selection for the QTL is possible, but the inverse effect on protein and oil content should be kept in mind.