Antibiotic resistance has become a primary concern in medicine because of the overuse and misuse of classical pharmaceuticals. Recently, nonbiological complex drugs (NBCDs) have gained interest for their complex pharmacological profiles. Bituminosulfonates, which have lately been tentatively allocated toward NBCDs, are pharmacologically well-studied and show low potential in resistance development. However, molecular composition knowledge is limited. With this work, we present a comprehensive approach to investigate the manufacturing process of complex pharmaceuticals like bituminosulfonates on a molecular level via Fourier-transform ion cyclotron resonance mass spectrometry. The application of various hyphenations and ionization techniques comprehensively covers the entire mass and polarity range of the matrix, and the high sensitivity enables the identification of significant and minor chemical alterations caused by the multistep manufacturing process. The distillation of the shale crude oil eliminates highly aromatic PAH and PASH constituents. ESI(-) revealed strong PAH- and PASH-sulfonate formation after reacting the shale oil distillate with sulfuric acid. Increasing alkylation reduced the sulfonation yield, instead causing oligomerization side reactions, as observed by APPI analysis. Furthermore, multidimensional gas chromatography coupled with high-resolution mass spectrometry verified core structural motifs. With this work, we demonstrate the high potential of FT-ICR MS in NBCD process analysis. The results also give valuable information for future pharmacological investigations focusing on specific compound classes or properties.