Boti Garcia, president of Spain's State Federation of Lesbians, Gays, Transsexuals and Bisexuals, and José María Núñez-Blanco, president of LGBT rights group the Triangle Foundation, were invited along with representatives of 350 other Non-Governmental Organizations (NGOs) and charities involved with social causes.
García admitted that she had been surprised to receive the invitation, noting: "We have asked more than once for meetings with the vice president of the government and he's never even answered."
Spanish daily Publico reported both representatives as having connected better with the queen, who was said to have spent more time with them than the king, and who had highlighted the importance of their presence at such an .
"We felt that our message had been listened to and understood, " said García.
She said that she had asked the queen to defend the human rights of people who may be persecuted for their sexual orientation in countries that the royal couple visit while official duties.
García added her hope that the meeting would "go beyond mere protocol" and lead the royal couple to adopt a "proactive defence" of human rights.
The attitude of Spain's new queen stands in stark contrast to that of her predecessor, Queen Sofia, who in 2008 declared herself opposed to same-sex marriages, leading to a statement of protest from the Triangle Foundation.
Letizia, who is said to have a close relationship with her mother-in-law, found herself in an awkward position but diplomatically described the old queen as "a woman of her time".