Performing the identification of organic chemical compounds from a set of spectroscopic data gives the opportunity to students to develop critical thinking and problem-solving skills. In this context, we developed a student-centered methodology for teaching molecular structural analysis to first-year undergraduate students. This systematic approach was implemented during classroom-training sessions and complemented by a home-based training program. Home-based activities involved a multiplatform Web-based application (ULg Spectra) combined with guided inquiries. ULg Spectra offers fully interactive tutorial/drill materials relying on mass, infrared, and nuclear magnetic resonance spectra (i.e., one-dimensional [superscript 1]H NMR and [superscript 13]C NMR spectra and two-dimensional [superscript 1]H-[superscript 13]C HSQC spectra). A survey indicates that the vast majority of students valued the ULg Spectra application combined with guided inquiries, especially in terms of usability and usefulness. This approach prompted them to actively engage in problem solving, and student autonomy was improved. Statistical data demonstrated that low-, medium-, and high-training students' groups showed increasing performance in the final exam. Interestingly, a statistically significant increase in final grades and success rate was also observed compared to previous years.