In his sophomore season, Malkin recorded his first NHL hat-trick, against the Toronto Maple Leafs, on 3 January 2008. He earned another three-goal performance several games later, on 14 January, against the New York Rangers. Midway through the season, when more heralded teammate and captain Sidney Crosby went down with an ankle injury, Malkin seized the opportunity to lead the Penguins, scoring 44 points in the 28 games Crosby was absent. In total, Malkin completed the season second in NHL scoring with 106 points, six points behind Alexander Ovechkin for the Art Ross Trophy. Malkin continued to dominate into the Stanley Cup playoffs as the Penguins made it to the 2008 Stanley Cup Final. He scored three points against the Detroit Red Wings in the finals, totaling 22 points overall, but the Penguins were defeated by Detroit in six games.
Malkin's sophomore season culminated in a Hart Memorial Trophy nomination as NHL MVP—the award was given to Ovechkin—and First Team All-Star honors. On 2 July 2008, with one year left in his entry-level contract, he signed a five-year, $43.5 million contract extension with Pittsburgh.
Malkin began the 2008–09 season by scoring his 200th NHL point with an assist to Sidney Crosby on 18 October 2008. The goal was also Crosby's 100th career goal and 300th career point. Crosby had a team trainer cut the puck in half so both players could commemorate the moment. Voted as a starter to the 2009 NHL All-Star Game later in the season, Malkin won the shooting accuracy segment of the Skills Competition, initially shooting four-for-four before beating Dany Heatley three-for-four in a tie-breaker. After having finished runner-up to Alexander Ovechkin the previous season for the Art Ross Trophy, Malkin captured the scoring championship with 113 points. He became the second Russian-born player to win it, after Ovechkin, and the fourth Penguin, after Mario Lemieux, Jaromír Jágr and Crosby. However, he would once again be runner-up to Ovechkin for the Hart Trophy, although this time garnering a few more first-place votes. In 2008, he had just one first-place vote (out of 134 votes) and 659 points to Ovechkin's 128 first-place votes and 1,313 points. In 2009, Malkin had 12 first-place votes (out of 133 votes) and 787 points to Ovechkin's 115 first-place votes and 1,264 points.