He was also the nephew of Beatriz de Bobadilla, marchioness of Moya [es] and of Peñalosa, a patron of Christopher Columbus and close friend to Queen Isabella.

In 1480 he was named knight commander of the Order of Calatrava in Auñón, Berninches, Castellanos y El Collado, which indicates that he was between 30 and 35 years old and possessed of some social standing, as this position would not have been given to someone young.

[1] On 21 May 1499, the Catholic Monarchs of Spain named him as a judge with orders to investigate reports from Hispaniola, namely numerous complaints about the policies of Christopher Columbus and his brothers which included accusations that they accepted bribes, enslaved the natives, under-paid the quinto real for pearls and gold, mishandled the rebellion of Francisco Roldán, and that they had committed treason.

[1] Francisco de Bobadilla began his investigation, basing it on the accusations that had made their way to the Spanish crown, and he gathered a large number of complaints against Bartholomew, Giacomo, and Christopher.

He would write in his father's biography that the Catholic Monarchs, seeing various factions in court alleging that payments were not being made and letters sent to Spain from people who were unhappy on Hispaniola, decided to send a judge to investigate what was happening.

During his tenure, he incentivized private enterprise and set a policy whereby natives would primarily work in gold extraction in the existing mines in Haina and Cibao.

According to Ferdinand Columbus, Bobadilla spent rents and royal tributes in order to win the population's favor, alleging that the Monarchs only wanted to possess the land and were unconcerned about anything else.

[7] He further claimed that Bobadilla auctioned off land that Christopher had obtained for the Monarchs below market price and gave natives to various rich and powerful people on the condition that they share their slaves' earnings with him.