Starting in 1995, a foot injury sidelined him for two years; he was diagnosed with rheumatoid arthritis. However, a German doctor successfully treated him. He was unable to compete in 1996.
In 1997 he returned to competition and won two tournaments and the Ryder Cup with the European team.
In April 1999, he won his second Masters at Augusta, which he dominated from the second day onwards, finishing the course eight under par for a total of 280, two ahead of Davis Love III. By ing as champion at the Masters Tournament, "Txema" Olazabal became the fourteenth player to win it twice or more.
In 1998, he won the Dubai Dessert Classic, a European Golf Tour tournament held at the Emirates Club, after overcoming both his rivals and the pharyngitis and fever that nearly forced him to withdraw from the tournament.
After his second "green jacket" with victory at the 1999 Masters at Augusta, his performance had declined. He only managed to hit 58% of his balls into the fairways and fell to 164th on the European tour. In 2000, he won the title at the Benson & Hedges in England. But José María Olazabal wanted to change his career and decided to play more tournaments on the United States circuit instead of the European one. So much so that in May 2001, he was crowned champion of the French Open and in December, the Hong Kong Open, where he made three birdies, shooting a 7-under-par 64 for a total of 22-under-par 262. A week earlier, he finished second in Taiwan. In this way, he continues to occupy an important place in the golf elite, as these successes allow the Hondarribia golfer to forget a drought that in recent years has left his record at rock bottom.