Because he signed a "bonus contract" when he became a professional player in 1954, Amalfitano spent the first two years of his pro career sitting on the bench of the New York Giants under the terms of the rule then in force.

He moved back to the Giants as a coach in 1972, then to the San Diego Padres from 1976–77, before rejoining the Cubs as a member of Herman Franks' staff in 1978–79.

The Cubs won only 26 games, losing 46, to remain in the basement of the National League East Division, but Amalfitano was allowed to return for 1981.

During that strike-shortened, split-season campaign, his team won a total of 38 games, losing 65, finishing last and next-to-last with the worst overall record in the division.

He then was a consultant with the Dodgers' baseball operations department and worked with minor league infielders in his original organization, the Giants, before assuming his current position with them.