The Dortmund trainer believes his colleague will be under pressure at the Allianz Arena and is confident Robert Lewandowski will continue to give his all for BVB
Heynckes guided Bayern to a historic treble in 2012-13 and many expect them to continue their dominance under the former Barcelona coach following his record of 14 trophies in four years at the Catalan giants.
But Klopp insists it will not be easy being the 68-year-old's successor at the Allianz Arena.
"There could definitely be more appealing working circumstances for a coach. It was rather obvious that it would be like this, though," he was quoted as saying by Bild.
Klopp then went on to praise Guardiola's humble attitude and made it clear he thinks the Spaniard will do a good job at the Bundesliga champions.
"I think that we are all just happy that Pep himself arrived at his unveiling by foot and didn't come hovering into the press room.
"Pep is the most extraordinary coach that comes into mind. He's a very nice guy and incredibly successful. That's not a bad thing for Bayern.
"And the team did not exactly get any worse compared to last season. So one should expect them to do reasonably well."
The BVB coach also had his say on the situation of Robert Lewandowski, who had set his sights on a move to Bayern, but was denied a switch to Dortmund's rivals by club CEO Hans-Joachim Watzke.
"I don't have any fear that Robert will no longer give his all. He has said that he wanted a transfer and where he wanted to go. That didn't materialise, but things like that happen," he added.
"The way I know him, there's hardly anyone who is a better professional. It's completely normal that we will not all stay at BVB for the next 100 years.
"Robert is still young and has room for improvement. He can make steps forward at his age and we want to help him achieve this."
Lewandowski's contract with Dortmund expires in 2014 and is widely expected to leave the club for Bayern on a free transfer next year.