Jurgen Klopp's men find themselves languishing 13th in the Bundesliga standings after seven matches, with Cologne one of only five teams below them in the table.
However, things are beginning to look up for Dortmund as their crippling injury list has started to ease with Gundogan and Reus both set to return.
Gundogan has been missing since August 2013 with a persistent back problem, while Reus injured his ankle against Scotland at the start of September, a similar issue to the one that kept him out of Germany's triumphant World Cup campaign.
Both players appeared for Dortmund in a friendly against Bochum's reserves on Friday and, after also playing in the win over fourth-division Viktoria Cologne in a training match on Tuesday, the duo are expected to feature in some capacity on Saturday.
Sporting director Michael Zorc told the club's official website: "Both of them [Gundogan and Reus] looked very good, especially when you consider how long Ilkay has been away.
"He looked very comfortable on the ball, but it was only his first test and it was only for one half so we shouldn't attach too much importance to it."
Dortmund's dreadful start to the season has seen them accumulate just seven points from a possible 21, with four of their seven matches so far ending in defeat.
Klopp, though, will have a psychological edge over Cologne on Saturday, having won all eight of his previous meetings against the Rhineland side since joining Dortmund in 2008.
Peter Stoger's side appeared to acclimatise to the Bundesliga fairly quickly following a draw with Hamburg and a 2-0 win at Stuttgart in their opening two matches.
But things have unravelled since and Cologne are currently on a run of three successive league defeats, while they also lost to fourth-tier side Alemannia Aachen in a recent friendly.
And Stoger is under no illusions as to the test that faces his side when Dortmund visit on Saturday, noting that regardless of who is or is not fit, Klopp will still have a team full of "world class" players.
Dortmund could have more than just Gundogan and Reus returning, too, with Henrikh Mkhitaryan, Sebastian Kehl (both foot) and Ji Dong-won (hamstring) all taking part in Tuesday's friendly following their respective injury problems.
Oliver Kirch (thigh) is also on the mend and is battling for his first league appearance of the season, claiming to be "90 per cent fit" and Shinji Kagawa should be fine despite a knock to the head on international duty, but Nuri Sahin (knee) remains on the sidelines.
Cologne, who have been training in Florida and Austria, have few injury concerns of their own, with the only doubt lingering over captain Miso Brecko after he picked up a slight knock for Slovenia.
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