A recent 1,000-page report complied by the United States Anti-Doping Agency accused the 41-year-old of running one of the most sophisticated doping programmes that the sport has ever seen.
As a result, Armstrong was stripped of his seven Tour de France titles and has been banned from competing for life by the International Cycling Union.
However, Indurain believes that the Texan will return one day to prove his innocence.
"Even now I believe in his innocence. He has always respected all the regulations. He has won all the cases he's had," said the Spaniard.
"What surprises me is that he doesn't keep fighting. I think he will come back and appeal and try to show that he played fair for all those years."
Following the news that he had lost his titles, Armstrong altered his Twitter bio earlier today.