The Latics sit dangerously close to the relegation zone and the Spaniard has underlined his desire to secure safety ahead of sealing a day out at Wembley in the cup
The Latics suffered a 4-0 defeat at the hands of Liverpool on Saturday which leaves them teetering above the top-flight drop zone by virtue of goal difference.
And, with an FA Cup quarter-final meeting with Everton approaching, the Spaniard has revealed that he would happily sacrifice a Wembley visit to avoid relegation.
"Success in the Cup is something we want, but never at the price that it would affect our league campaign. That’s something I will never allow to happen," Martinez told reporters.
"Our situation is a dangerous one and the position we are in after losing to Liverpool means we need to find the best possible team to carry on playing in the league."
The likes of Callum McManaman, Roman Golobart and Fraser Fyvie have played prominent roles in Wigan's cup run and Martinez hinted at keeping faith in his youngsters.
"The Cup game will give us the opportunity to make changes," he explained.
"Not to rest people, but maybe to find people who deserve to be in the team and to develop real competition.
"It’s a difficult game at Everton but one game away from Wembley is a great opportunity. In the position we’re in, after this we need to find the best possible team to carry on playing in the league.
"Those who have played in the Cup deserve an opportunity and need to show what they can do against Premier League opposition.
"Cup runs with 11 players affect performances because it’s impossible to maintain the level of players.
"But if you have a big enough squad, you can share demands and success in the Cup which can help in the league. That is what we have had this season. The FA Cup has helped towards the league."