"What naturalization does is provide the asylum-seeker another layer of protection", she said.
Assange (46) was granted political asylum in the embassy when Swedish prosecutors were investigating sex crime allegations against him.
Swedish prosecutors previous year unexpectedly dropped their investigation into allegations against him, which included a claim of rape.
The new citizenship status is not expected to make a big difference for Mr Assange in the near future, as any movement outside the embassy must still be reported to United Kingdom authorities.
Britain recently rejected Assange's bid for diplomatic status, leaving it to Ecuador to try and find a more permanent resolution than having Assange living in its embassy indefinitely.
On Wednesday, Assange hinted that something was afoot when he tweeted a picture of himself wearing a yellow Ecuadorean soccer jersey.
Jérémie Zimmermann, a friend and former colleague of Assange, wrote in 2012 that "unless the people around him force him into the shower, he might not change his clothes for days".
Assange still faces arrest for breaching bail conditions if he steps outside the embassy. She said that Ecuador formally requested that Assange be given diplomatic status December 20 and that Britain rejected the request the following day.
"Of course whatever alternative (taken) will be made strictly following to the norms and procedures of global law, in coordination with the United Kingdom, a country which we maintain the best relations of friendship and cooperation", Ms Espinosa said.
Espinosa expressed irritation at recent news reports, saying she felt "obliged to make statements about a matter" that needed to "be managed with prudence and caution".
Reuters found an entry for "Julian Paul Assange" in Ecuador's Civil Registry, which only includes Ecuadorean citizens.
A United Nations panel concluded in 2016 that Assange was under arbitrary detention.