This study was focused on distinguishing of genetically modified organism (Monsanto 89788 variety) and conventional soybeans by employing high-resolution mass spectrometry (HRMS) techniques for non-target screening of sample extracts. Two hyphenated instrumental platforms represented by (i) ultrahigh-performance liquid chromatography (U-HPLC) coupled to quadrupole/time of flight and (ii) ambient mass spectrometry with direct analysis in real time (DART) ion source-coupled OrbitrapMS were used. The statistical processing of generated data (metabolomic fingerprints) was performed by multivariate data analysis; principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) showed that both employed techniques enabled correct classification of genetically modified and conventional soybeans. In addition, some phosphatidylcholines and sugars were identified as the most significant markers.