During spring training in 1961, following advice from Pirates' batting coach George Sisler, Clemente tried to modify his batting technique by using a heavier bat to slow the speed of his swing. During the 1961 season, Clemente was named the starting NL right fielder for the first of two All-Star games and went 2 for 4; he hit a triple on his first at-bat and scored the team's first run, then drove in the second with a sacrifice fly. With the AL ahead 4–3 in the 10th inning, he teamed with fellow future HOFers Hank Aaron, Willie Mays, and Frank Robinson to engineer a come-from-behind 5–4 NL victory, culminating in Clemente's walk-off single off knuckleballer Hoyt Wilhelm. Clemente started again in right field for the second All-Star game held that season and was 0 for 2, flying and grounding out in the 2nd and 4th innings. That season he received his first Gold Glove Award.
Following the 1961 season, he traveled to Puerto Rico along with Orlando Cepeda, who was a native of Ponce. When both players arrived, they were received by 18,000 people. During this time, he was also involved in managing the Senadores de San Juan of the Puerto Rican League, as well as playing with the team during the major league off-season. During the course of the winter league, Clemente injured his thigh while doing some work at home but wanted to participate in the league's all-star game. He pinch-hit in the game and got a single, but experienced a complication of his injury as a result, and had to undergo surgery shortly after being carried off the playing field. This condition limited his role with the Pirates in the first half of the 1965 season, during which he batted .257. Although he was inactive for many games, when he returned to the regular starting lineup, he got hits in 33 out of 34 games and his batting average climbed up to .340. He participated as a pinch hitter and replaced Willie Stargell playing left field during the All-Star Game on July 15.
Clemente was an All-Star every season he played in the 1960s other than 1968—the only year in his career after 1959 in which he failed to hit above .300—and a Gold Glove winner for each of his final 12 seasons, beginning in 1961. He won the NL batting title four times: 1961, 1964, 1965, and 1967, and won the league's MVP Award in 1966, hitting .317 with 29 home runs and 119 RBIs. In 1967, Clemente registered a career high .357 batting average, hit 23 home runs, and batted in 110 runs. Following that season, in an informal poll conducted by Sport Magazine at baseball's Winter Meetings, a plurality of major league GMs declared Clemente "the best player in baseball today," edging out AL Triple Crown winner Carl Yastrzemski by a margin of 8 to 6, with one vote each going to Hank Aaron, Bob Gibson, Bill Freehan and Ron Santo.