Zobel was born in Seville, Spain, on October 9, 1877 to Jacobo Zobel y Zangroniz and Trindad de Ayala y Roxas. He had a twin named, Alfonso, who died the age of five. His other siblings were Fernando Antonio, Margarita and Gloria (who died a few months after her birth).
He studied at the Colegio de San Juan de Letran. He received a bachelor of arts degree from Real Colegio Alfonso XII in El Escorial, Spain. He pursued postgraduate studies at Liceo de San Luis and the College Sainte-Barbe, Paris. He was very much interested in engineering and mining, so he also took courses at the Ecole Nationale Superieure des Mines de Paris, Paris from 1897 to 1901. He also pursued the study of painting in the French capital.
When he returned to Manila in 1901, he married his cousin Consuelo Roxas de Ayala on October 16, 1901. They had three children - Jacobo (father of Enrique J. Zobel), Alfonso (father of Jaime Zobel de Ayala) and Mercedes. The union was short-lived after Consuelo succumbed to cholera in September 25, 1907 at the age of 30.
He was a widower for three years when he met Fermina Montojo de Torrontegui. She was the daughter of the Spanish admiral Patricio Montojo, who led the Spanish fleet against Commodore George Dewey in the Battle of Manila Bay. They were married on November 12, 1911 and had four children - Matilde, Consuelo, Gloria, and Fernando (and namesake of his brother), who would become the famous modern painter.
He was a managing partner of Ayala y Compania from 1901 to 1913 and from 1920 until 1943.
In 1914, his children from Consuelo - Jacobo, Alfonso and Mercedes - would inherit Hacienda de San Pedro de Macati from his aunt (and mother of Consuelo), Carmen Roxas de Ayala. The property was first purchased in 1851 by his great uncle, Jose Bonifacio Roxas, for 52,800 pesos. It was inherited by Roxas' son, Pedro Pablo Roxas (and upon his death in 1912, by his widow, Carmen). In 1929, ownership of the property would be transferred to Ayala y Compania. The property - which had lain in the family’s hands, undeveloped and undisturbed for several decades - would serve as the basis of his family's future wealth. During the 1930s, portions of the property would be developed, as the company's initial foray into real estate development. In 1937, he offered 42 hectares of the property to be leased for the development of Nielson Field.
On June 21, 1924, the Ayala distillery (Destileria y Licoreria de Ayala y Compania, maker of Ginebra San Miguel) was sold by Ayala y Compania to La Tondena Inc.
Aside from his involvement with the Ayala company, he also established La Porcelanica in 1903 - the first ceramics factory in the Philippines. The following year, he established a glass factory with Eduardo Soriano (father of Andres Soriano Sr.). He co-founded Filipinas Compania de Seguros in 1913 and ventured into insurance and finance as vice president of Insular Life Assurance Company, a director of Philippine Guaranty Co. and a director of Banco Espanol-Filipino.
Zobel inherited the liberal ideas and interests of his father Don Jacobo Zobel y Zangroniz. Like his father, he was educated in Europe, not only in business and sciences, but also in the arts. He loved the cultivation of the arts and culture. His mansion on Plaza del Carmen and Leon Guerrero Street in Ermita, Manila became the focal point of many tertulias and salon de artistas. He donated his vast collection of books on European literature to the University of the Philippines library.
He was the first modern Hispanist and founded Premio Zobel in 1929 in order to preserve and promote the use of the Spanish language, which he believed was the true language of Filipino nationalists. His great obsession was the conservation of the spiritual ties between Spain and the Philippines through the promotion of its language and culture. The Premio Zobel was the fulfillment of his desire that "No quiero que el espanol muera en Filipinos". Today, Premio Zobel is administered by his grandchildren, Georgina Padilla MacCrohon and Alejandro Padilla (both children of his daughter, Gloria).
Together with brother Fernando Antonio, he co-founded Casino Espanol de Manila, a socio-civic club for Hispano-Filipinos. He established the Patronato Escolar Espanol and the Asociacion Pro-Idioma Hispano, both efforts directed at strengthening the role of Spanish in the educational system. He was a founding member of Academia Filipina de la Lengua Espanola in 1924, which became the correspondent of the prestigious Real Academia de la Lengua Espanola.
He dabbled as a Spanish-language publisher when he resuscitated the moribund El Mercantil. He supported the arts and gave scholarships, among them, a young Fernando Amorsolo, who in gratitude would teach his son, Fernando, the rudiments of art.
In 1930, he helped fund the construction of the Manila Metropolitan Theater, a landmark art deco building designed by Juan Arellano. He became the treasurer of the Metropolitan Theater Company.
In 1936, he reported the discovery of a horde of Oriental pottery found on his Calatagan, Batangas property to the National Museum director Eduardo Quisumbing and subsequently funded the ensuing excavations.
In April 1939, he was appointed by General Franco as the acting consul for Spain in the Philippines. The government of Spain, in admiration of his many philanthropic and cultural causes, awarded him La Gran Cruz Isabela la Catolica and the Medalla del Merito Civil.
Zobel died on February 17, 1943 in Manila, at the height of the Japanese Occupation during World War II.