Liebig married Henriette "Jettchen" Moldenhauer (1807–1881), the daughter of a state official, in May 1826. They had five children, Georg (1827–1903), Agnes (1828–1862), Hermann (1831–1894), Johanna (1836–1925), and Marie (1845–1920). Although Liebig was Lutheran and Jettchen Catholic, their differences in religion appear to have been resolved amicably by bringing their sons up in the Lutheran religion and their daughters as Catholics.
Liebig and several associates proposed to create an institute for pharmacy and manufacturing within the university. The Senate, however, uncompromisingly rejected their idea, stating that training "apothecaries, soapmakers, beer-brewers, dyers and vinegar-distillers" was not the university's task. As of 17 December 1825, they ruled that any such institution would have to be a private venture. This decision actually worked to Liebig's advantage. As an independent venture, he could ignore university rules and accept both matriculated and unmatriculated students. Liebig's institute was widely advertised in pharmaceutical journals, and opened in 1826. Its classes in practical chemistry and laboratory procedures for chemical analysis were taught in addition to Liebig's formal courses at the university.
One of Liebig's frequent collaborators was Friedrich Wöhler. They met in 1826 in Frankfurt, after independently reporting on the preparation of two substances, cyanic acid and fulminic acid, that apparently had the same composition, but very different characteristics. The silver fulminate investigated by Liebig, was explosive, whereas the silver cyanate found by Wöhler, was not. After reviewing the disputed analyses together, they agreed that both were valid. The discovery of these and other substances led Jöns Jacob Berzelius to suggest the idea of isomers, substances that are defined not simply by the number and kind of atoms in the molecule, but also by the arrangement of those atoms.