Apart from his more comprehensive works, his most important palaeontological contributions are perhaps his observations on the structure of the treelike lycopodiopsid, Sigillaria, an extinct plant related to the living club mosses, and his researches (almost the last he undertook) on fossil seeds, of which a full account was published posthumously in 1880.

Among his achievements in this direction, the most notable is the treatise Sur la génération et le développement de l'embryon des Phanérogames ("On the generation and development of the spermatophyte embryo"), which is remarkable for the first account of any value of the development and structure of pollen, along with the confirmation of Giovanni Battista Amici's 1823 discovery of the pollen-tube, the confirmation of Robert Brown's views as to the structure of the unimpregnated ovule (with the introduction of the term "sac embryonnaire", or embryo sac), showing how nearly Brongniart anticipated Amici's subsequent (1846) discovery of the entrance of the pollen-tube into the micropyle, fertilizing the female cell, which then develops into the embryo.

His systematic work is represented by a large number of papers and monographs, many of which relate to the flora of New Caledonia; and by his Énumération des genres de plantes cultivées au Muséum d'histoire naturelle de Paris (1843), a catalogue of the plants in cultivation at the French National Museum of Natural History; it is a landmark in the history of classification in that it forms the starting-point of the classification system, modified successively by Alexander Braun, August W. Eichler and Adolf Engler, which was not superseded until the development of DNA research.

In addition to his scientific and professorial labours, Brongniart held various important official posts in connection with the department of education, and interested himself greatly in agricultural and horticultural matters.

With Jean Victoire Audouin and Jean-Baptiste Dumas, his future brothers-in-law, Brongniart founded the Annales des Sciences Naturelles, a peer-reviewed journal, in 1824.