According to his biographer María Belén Bañas Llanos, Juan de Cuéllar was born in Aranjuez into a family employed in the care of plants in the royal gardens.
In 1783 and 1784, he attended classes at the Real Jardín Botánico de Madrid, in a program to impart scientific knowledge to pharmacists.
The El Peruano had arrived in Cádiz on February 21, 1785, carrying part of the scientific material sent back from Peru and Chile by the royal expedition under Hipólito Ruiz and José Antonio Pavón.
The Company asked the minister of the Indies, José de Gálvez to name a botanist to investigate the flora of the islands.
Gálvez turned over the task to Casimiro Gómez Ortega, head of the Real Jardín Botánico de Madrid.
This was a scientific expedition at the same level as that of Ruiz and Pavón, and Cuéllar asked the king to give him the title of botánico real (royal botanist).
The first specimens sent back were natural products of the Philippines, including seashells, seeds, resins, woods, drawings, minerals, and some living plants.
A royal order dated in January 1788 directed him to promote the cultivation of cinnamon and nutmeg, in a last attempt to break the Dutch commercial monopoly on these spices.