Although during the last decades the philosophy of chemistry has greatly extended its thematic scope, the main difficulties appear in the attempt to link the chemical description of atoms and molecules and the description supplied by quantum mechanics. The aim of this paper is to analyze how the difficulties that threaten the continuous conceptual link between molecular chemistry and quantum mechanics can be overcome or, at least, moderated from the perspective of BM. With this purpose, in “The quantum-mechanical challenges” section (...) the foundational incompatibility between chemical and SQM descriptions will be briefly recalled. “Bohmian mechanics” section will be devoted to explain the main features of BM. In “Empirical equivalence and underdetermination” section, the consequences of the empirical equivalence between SQM and BM will be discussed. Finally, in the Conclusion, we will stress the scope of the obtained conclusions and the philosophical difficulties that still remain even after adopting BM for foundational purposes. (shrink)