In 1988, Johnson did not nearly live up to his stellar 1987 season, but still showed decent home run power. He reverted to hitting much better from the left side with a .183 average and .338 slugging from the right side. A mid-season injury to his right shoulder contributed to his poor offense. One bright spot was September 8, 1988, when he had the only five-hit game of his career, going 5-for-5 with a three-run home run and four RBIs in a Wrigley Field victory. While Johnson was struggling to stay above .230, the Mets tried out 21-year-old third-base prospect, Gregg Jefferies, who blazed through September. After 13 games, Jefferies, who was also a switch hitter, had a batting average of .462 and a fantastic slugging percentage of .962 with five home runs, a four-hit game and four three-hit games. Despite Johnson's mediocre season, the Mets easily coasted to a division win but Johnson went 1-for-18 with six strikeouts in the 1988 NLCS. With the heavily favored Mets down 3–2 in the series, he was benched for Games 6 and 7 in favor of Jefferies. Johnson pinch-hit in Game 7 and struck out for the final out of the Mets disappointing season.