His veiled attack on the economic and Indigenous policy of Visitador (Royal Inspector) José Antonio de Áreche was unprecedented.

Baquíjano was a mercantilist economic thinker, although he was also influenced by the English economist Josiah Child, a qualified exponent of free trade.

Baquíjano believed that free trade and the separation of the Viceroyalty of Río de la Plata were the causes of the economic crisis in Peru at the end of the eighteenth century.

He led a reformist group at the University, arguing for the replacement of Scholasticism with the thought of men such as Descartes, Newton and Juan Heinecio.

In the Mercurio, Baquíjano published histories of the Audiencia of Lima, of the University, and of the mines in Potosí, as well as a dissertation on the economy of Peru.

In 1793 he became president of the Sociedad Académica de Amantes del País (Academic Society of Lovers of the Country).

He criticized the Spanish policy against the insurgents in Peru, calling it foolish and arguing for an end of hostilities.