Boateng, who joined Bayern from Manchester City in 2011, has been a key member of the Bayern side that are on a run of five consecutive Bundesliga titles.
But a thigh injury sustained at Euro 2016 preceded a campaign ravaged by fitness problems last time around, with the 29-year-old restricted to 13 Bundesliga appearances.
In an interview with Kicker, Boateng explained he was left pondering whether it was time for a fresh start and took his concerns to the Bayern board during Carlo Ancelotti's time in charge.
"I had a conversation with the directors about how they see me in the summer, I said I was thinking about it [a transfer]," he said.
Asked about the reason why he did not play in a couple of important matches under former boss Ancelotti, Boateng added: "Maybe because I played not that much with him as coach, he saw me too less because of my injuries."
Boateng was not in Bayern's squad for their 3-0 Champions League to Paris Saint-Germain last month and Ancelotti was axed the following day.
With Heynckes – who oversaw Bayern's treble in 2013 – back for a fourth term in charge, which he kicked off with a 5-0 rout of Freiburg on Saturday, Boateng said: "His attitude that he wants to give something back to FC Bayern is very positive for us as a team.
"There are not many managers who have such a keen sense of how to deal with players, their approach, their training, their motivation."
Photo Bongarts. Caption: Bayern Munich defender Jerome Boateng