The periodic table is an icon of chemistry and an essential component of every school curriculum. However, the fundamental concepts underpinning this extraordinary scientific framework are often overlooked in both schools and universities due to their deceptive simplicity. Even the transition from atomic weight to atomic number as the basis for organizing elements is sometimes glossed over in textbooks with a few oversimplified sentences. This work aims to provide teachers with an overview of the 19th-century debates among eminent chemists over three key notions central to Mendeleev’s system: atomism, atomic weight, and the nature of elements. Furthermore, we illustrate that the transition to a new organizing principle was not a sudden shift but an extended process requiring new experimental data, updated atomic models, and a great deal of imagination. We also highlight the fact that the introduction of atomic number sparked a paradigmatic shift in the periodic system; it provided Mendeleev’s construction with a more solid foundation by anchoring it to the atom’s internal structure and ultimately led to a redefined concept of a chemical element.