He was appointed ambassador to Taiwan in December 1999 and served in that position until he became Minister of Foreign Affairs on March 30, 2004, a position he held until January 2006. He resigned the position due to controversy over how aid money from Morocco was spent. São Tomé and Principe’s government called Pequeno’s use of funds “improper.” And said that "as government, the Foreign Affairs Minister is hierarchically subordinate to the Prime Minister, before whom he has the duty to inform and the obligation of loyalty, leaving no room for secrecy.” Pequeno used 407,000 euros (about 488,000 US dollars) to buy goods, equipment and protocol vehicles. He said that he had spent the money on the president’s behalf and denied taking any for himself.

 

He was later appointed Permanent Representative to the United Nations. On November 20, 2007, Pequeno replaced Carlos Gustavo dos Anjos as Minister of Foreign Affairs.