Injuries to first-choice players have been debilitating, but the team is struggling to gel and unable to find the X-factor that made them so strong in 2012 and 2013.
The loss of Radamel Falcao Garcia to injury is an enormous blow to Colombia, but the effect will not be so much on the team's finishing but on their approach play.
Carlos Bacca and Teofilo Gutierrez, who are likely to start against Greece, are both capable strikers but rely much more on service from midfield for their goals. Bacca in particular often has a heavy touch.
Aside from Falcao, Colombia have been unfortunate to lose vice-captain and defender Luis Amaranto Perea as well as midfielder Edwin Valencia to injuries. Perea will be missed for his leadership qualities, but Fluminense's Valencia is a crucial link between defence and attack, able to kick-start counter-attacks with good passing.
Furthermore, a knock to Aldo Leao Ramirez has left Colombia very short of passing midfielders in front of the back four. For a side who also rely on two of these centrocampistas to cover for the rampaging runs of their fullbacks, this is a severe blow to the team's chemistry.
There are also concerns over the form and fitness of the two first-choice fullbacks. Napoli's Camilo Zuniga, out since October with a "mystery" injury, has looked adept going forward but slow going back.
With these problems, more pressure is placed on the young shoulders of starlet James Rodriguez. His level-headed approach, combined with a natural flair, should be the blueprint for Colombia at the World Cup.
Indeed, writing in the Daily Mail, Rio Ferdinand correctly assessed Rodriguez's skills but also the void left by Falcao and how this will affect Rodriguez's game:
He’s that rare talent — someone who gets you off your seat. The only downside is that clubmate and Colombia co-star Radamel Falcao is out injured. Falcao would have created the space for Rodriguez to thrive. But then the absence of Falcao is perhaps Rodriguez’s chance to take centre stage.
All is not well then, for Los Cafeteros, but they are hardly the only team struggling as they prepare for the 2014 World Cup in Brazil.
They are talented, but Colombia are a confidence team and need to win their first match at the tournament to avoid coming under significant pressure.
As a result, it is imperative that Pekerman has ironed out the team's problems before they take on Greece in Belo Horizonte on Saturday.