He was the only son in a family of three children of the German immigrant Jacobo Zóbel and the Spanish Ana Zangróniz, a daughter of a judge of the Real Audiencia of Manila.
[5] His father worked in Manila as a pharmacist, with his own pharmacy under the name Botica de Don Jacobo Zóbel on Calle Real in Intramuros.
His grandfather, Johannes Andreas Zóbel, arrived in the Philippines from Hamburg, Germany in 1832, together with his wife, Cornelia Hinsch, and their son, Jakob.
He befriended the young numismatist Don Antonio Delgado (1805–1879) from Madrid, who inspired his scholarship on antiquarian coins.
[9] From early 1866, Zóbel took over the management of the Botica from his father, who died at sea between Europe and the United States in November of that year during a voyage with one of his sisters.
Zóbel was mayor of the city of Manila for a time during the period of Governor-General Carlos María de la Torre y Navacerrada.
[12] During his term, Zóbel introduced many liberal reforms: public schools, the first tree-planting activities and campaigned for representation in the Spanish Cortes and also promoted equal opportunity for all Filipinos, Creoles or natives alike.
The couple decided to live briefly in Spain after Jacobo decided to study transportation systems in Europe, and he renewed his numismatic research, publishing a major work entitled Estudio Histórico de la Moneda Antigua Española Desde Su Origen Hasta El Imperio Romano in 1878 ( Historical Study of Ancient Spanish Coins from Their Origin to the Roman Empire).
Eventually, he built four other major tram lines in Manila and its vicinity (Malate, Sampaloc to Tondo), drawn by horses.