His following season was the one where he started to gain global recognition among football fans and critics alike. He scored 12 goals in 17 league matches, and even though the club finished third, they won the Taça de Portugal against Vitória de Setúbal, with Eusébio scoring two goals in the final. In that same season, he won the European Cup, also scoring two goals in the final against Real Madrid in a 5–3 result to Benfica. Due to his fine form during the season, he finished second in the 1962 Ballon d'Or, in his first complete season as a professional. In October 1963, he was selected to represent the FIFA team in the "Golden Anniversary" of The Football Association at Wembley Stadium.
He received a number of individual accolades and awards while playing for Benfica. He was the 1965 European Footballer of the Year (Ballon d'Or) and finished as runner-up twice, in 1962 and 1966, and in 1968 was the first winner of the Golden Boot Award, as Europe's leading scorer, a feat he repeated five years later. He was the Portuguese First Division's top scorer seven times (1964, 1965, 1966, 1967, 1968, 1970 and 1973), helping Benfica to win 11 Primeira Liga (1960–61, 1962–63, 1963–64, 1964–65, 1966–67, 1967–68, 1968–69, 1970–71, 1971–72, 1972–73 and 1974–75), 5 Portuguese Cup wins (1961–62, 1963–64, 1968–69, 1969–70 and 1971–72), 1 European Cup win (1961–62) and 3 European Cup finals (1962–63, 1964–65 and 1967–68).