The first version of LANaPDB comprised 12,959 compounds. This reported update includes 619 new compounds, resulting a total of 13,578 compounds in its second version published in early 2024. A new dataset was included: NPDB EjeCol which contains NPs from foods and plants isolated and characterized in Colombia, from the Coffee Region (Eje Cafetero). Moreover, the database was updated with new NPs from Costa Rica (NAPRORE-CR) and Mexico (BIOFACQUIM). Table shows the ten Latin American NP databases currently contained in LANaPDB. Initially, 1,707 compounds were considered for the update of LANaPDB from the two updated databases BIOFACQUIM, NAPRORE-CR, and the new database NPDB EjeCol. Nevertheless, from the initial 1,707 compounds, 1,088 molecules were duplicates and were no longer included. The remaining 619 molecules were added to LANaPDB.