He also studied botany at the Migas Calientes Botanical Gardens (now the Real Jardín Botánico de Madrid), under the supervision of Casimiro Gómez Ortega (1741–1818) and Antonio Palau Verdera (1734–1793).

The French physician Joseph Dombey was named as his assistant, and the pharmacologist José Antonio Pavón y Jimenez was also appointed.

One of the medical remedies brought back by this expedition was the boiled spouts of the quisoar plant, Buddleja incana, which was used to cure colds or, mixed with urine, to alleviate toothache.

Unfortunately, a part of the collection consisting of 53 crates with 800 illustrations, dried plants, seeds, resins and minerals was lost when the ship transporting it was wrecked on the coast of Portugal.

[2] The journals Ruiz produced for his exploration of South America during these years are remarkable for their breadth of ethnobotanical and natural history knowledge.

[citation needed] Genera of plants first named by Ruiz & Pavón, or containing species named by them, include the following:[3] The four expeditions authorized by King Carlos III to the Spanish colonies were those of Ruiz and Pavón to Peru and Chile (1777–88); José Celestino Mutis to New Granada (1783–1808); Juan de Cuéllar to the Philippines (1786–97); and Martín Sessé y Lacasta to New Spain (1787–1803).