In 1942, Waitkus earned promotion to the AA Los Angeles Angels of the Pacific Coast League. In 175 games, he tallied a league-leading 235 hits, as well as 40 doubles, 81 RBI, and a .336 average.

From 1903 through 1957, the Los Angeles Angels, a minor league baseball team, were one of the mainstays of the Pacific Coast League, winning the PCL pennant 12 times. The Angels, along with the Portland Beavers, Oakland Oaks, Sacramento Solons, San Francisco Seals, and Seattle Indians were charter members of the Pacific Coast League which was founded in 1903.

When Wrigley could not get the city of Los Angeles to make the improvements to Washington Park he requested, he began construction of his own 21,000-seat stadium, appropriately named Wrigley Field, at 42nd Place and Avalon Boulevard in what is now known as South Central Los Angeles.

The Angels began play at Wrigley in 1926, and responded by winning their eighth PCL pennant, finishing 10½ games ahead of the second-place Oakland Oaks.

The team won pennants in 1938, 1943, 1944, and 1947, with the 1943 team being considered among the best in minor league history.

With the nation at war, Waitkus spent the next three years in the Marine Corps. He participated in several key Pacific Theater campaigns, including Bougainville and Luzon, earning four Bronze Stars.