The world number 26 has been plagued by injury woe during 2014 and is set to miss his second slam of the season.
A shoulder complaint meant the 28-year-old sat out the Australian Open, while his latest setback also saw him retire during his first-round clash with Jack Sock at last month's French Open.
Almagro was looking to go beyond the third round for the first time at Wimbledon and was seeded for the grass-court tournament.
Canada's Vasek Pospisil will now take the Spaniard's place among the seeds.
"Nicolas Almagro has withdrawn from Wimbledon 2014 with a foot injury," read a statement on Wimbledon's official Twitter account. "He is replaced in the seeds by Vasek Pospisil."
Novak Djokovic was announced as the top seed for the tournament on Wednesday, with Rafael Nadal second and defending champion Andy Murray third.