Lindor was replaced in the lineup by Brett Baty, who entered at third base and pushed Bo Bichette over to short.
Lindor was 2-for-2 with an RBI before exiting.
The news comes for the Mets as they try to snap a 12-game losing streak.
Star outfielder Juan Soto just returned to the lineup on Wednesday after going on the injured list on April 3 with calf tightness of his own.
Lindor has struggled to begin the 2026 season. After his two hits against Minnesota, he owns a .226/.314/.355 slash line with two homers. However, he had recently appeared to be hitting his stride offensively, with hits in 10 of his last 15 games.
New York’s skid has left it at the bottom of the NL East with a 7-16 record.