Benchtop nuclear magnetic resonance (NMR) spectroscopy has enabled the monitoring and optimization of chemical transformations while simultaneously providing kinetic, mechanistic, and structural insight into reaction pathways with quantitative precision. Moreover, benchtop NMR proton lock capabilities further allow for rapid and convenient monitoring of various organic reactions in real-time, as the use of deuterated solvents is not required. The complementary role of 19F NMR-based kinetic monitoring in the fluorination of bioactive compounds serves many benefits in the drug discovery process, since fluorinated motifs additionally improve drug pharmacology. In this study, 19F NMR spectroscopy was utilized to monitor the synthesis of novel trifluorinated analogs of monastrol, a small molecule kinesin Eg5 inhibitor, and to probe the mechanism of the Biginelli cyclocondensation, the multicomponent reaction used to synthesize dihydropyrimidine scaffolds. After isolating a trifluorinated hexahydropyrimidine product that did not dehydrate through the Biginelli cyclocondensation, we underwent this final step to obtain 6-trifluoromonastrol. This workflow was also applied to the synthesis of a trifluorinated analog of LaSOM 63, a compound previously reported to induce apoptotic cell death through the inhibition of ecto-5’nucleotidase activity. To further our studies, we used computational approaches to model the energetic pathways for the final dehydration in the formation of monastrol, LaSOM 63, and their respective trifluorinated analogs. Here, we present discoveries regarding the application of benchtop 19F NMR spectroscopy to provide high resolution reaction kinetics and mechanistic insight into the Biginelli reaction.