Having topped their group, Everton are looking to take a lead back to Goodison Park for the second leg.
However, Martinez admits the pitch at the Stade de Suisse gives him cause for concern, so much so that Arouna Kone will not feature despite playing 90 minutes with the Under-21s recently.
"It is a completely different surface and obviously the home team are used to it," said the Spaniard. "But we have prepared accordingly
"The recovery time after playing on this surface takes longer. So we have to manage the squad accordingly but we have strength in depth.
"There is no change to our mentality. We have approached each game individually. The game is a unique one."
Despite his concerns Martinez is keen to progress in the competition, but knows they face a tough task to get past the Swiss side.
He added: "For us to be involved to be in the Europa League is a great opportunity for us to grow as a club, particularly for the young players.
"We embrace this competition.
"I have been impressed and surprised with Young Boys' form. They have won eight of their last nine. They use the astroturf well.
"They have been very strong in Europe, particularly at home. We know they are going to be very tough."
