The new generations of the Digital Era have an interactive and agile language and way to communicate. On this regard, it is important to innovate in the teaching methods, and take advantage of the capacities that they possess. The aim of the present work was to develop an interactive platform, implemented as a website, which can be used by university students in engineering and science, to learn the stoichiometry of reactions, and understand the structures of chemical molecules, through 3D printing. The methodology consisted of two main objectives: 1) the development of interactive software to formulate balanced hypotheses, in the format for the website, and 2) the 3D design of molecules. The molecules were designed automatically, using as a base the molecules designed on the website of free use MolView, and others using the Valence shell electron pair repulsion (VSEPR) theory. An interactive platform called “3D Chemistry” has been developed, in which all possible reactions can be found, the student enters the reactants and the products of the reaction, and by means of an algorithm three stoichiometric coefficients can be obtained, with one correct alternative. The student must choose the correct alternative, to have access to visualize the molecules in an image with 3D design, and download the file for the MakerBot 3D printer, and in this way understand its spatial geometry and structure.