Though Connor had success in his season with the PL, the league struggled. Some of the teams ran into financial difficulties. National League teams rescheduled many of their games to conflict with PL games in the same cities, and a high number of PL games were cancelled late in the season due to rainouts. Connor was optimistic that the league would be successful in 1891, but it officially broke up that January.
Returning to the NL Giants for a season in 1891, Connor hit .294. In the offseason before 1892, Connor signed with the Philadelphia Athletics. The team broke up shortly after Connor signed, and his contract was awarded to the Philadelphia Phillies for that year. He returned to the Giants in 1893, raising his average to .322 and hitting 11 home runs. During the 1894 season, the Giants looked toward the team's youth and Connor lost his starting position to Jack Doyle. He was released that year and picked up by the St. Louis Browns. The next year, his brother Joe Connor made his major league debut with the same team. Joe played two games with St. Louis before being sent back down to the minor leagues. That year's St. Louis team finished with a 39-92 record, 48 ⁄2 games out of first place.