Now four years behind schedule and running at twice the original budget of €2.4 billion – even reported total earnings of some €750,000 won't make for an easy ride for Mehdorn's successor as CEO.
Talking to the Berliner Zeitung, Mehdorn, 72, said he was subjected to unacceptable "bullying" before he met with the BER supervisory board on Friday to outline plans to seek funds for a third terminal at the already undersized facility.
"I was bullied before the board meeting. They were already speculating about my successor. That was poor form," Mehdorn was quoted as saying in Tuesday's edition of the paper.
As an "old timer" he no longer felt constrained to go with the flow, he added. But he also felt conflicted by his decision to step down "because it does not reflect my sense of obligation or my personal goals".
Another source of contention was the sudden external auditing of all project documentation relating to Mehdorn's tenure, which started in March 2013.
Persistent mismanagement and corruption scandals around the project already took down Berlin's Mayor Klaus Wowereit, who resigned this month after 13 years in office.
Shake-ups to deepen old problems?
Berlin's acting mayor Michael Müller, who also represents the BER project owners, has now called for a reshuffle of the BER supervisory board and management.
But replacing the CEO can also deepen the problems facing the airport.
"This constant turmoil enormously complicates effective control by the supervisory board," Berlin interior senator Frank Henkel said after Mehdorn stepped down.
The board still supported the new opening schedule for the second half of 2017, said its deputy chairman Rainer Bretschneider, who is leading the body after Wowereit's departure.
Mehdorn, who previously ran the national rail carrier Deutsche Bahn and the Air Berlin airline, stood by his achievements during his tenure.
"We have a completely new management team," he said. "We have completely revamped the whole enterprise, the construction site, the controlling and reporting. Now we are a completely normal company."
While his resignation brought praise for his work from Transport Minister Alexander Dobrindt downward, no firm candidates for successor have emerged, however.
€128 per board sitting - any takers?
Meanwhile, the 15-member board must also select a new chairman after Wowereit's departure.
Last week it welcomed another industrial heavyweight into its midst with the arrival of former Daimler and Rolls Royce Germany chief Axel Arendt.
Already active in BER as city airspace economic development supervisor, 65-year-old Arendt was not easily persuaded to join the board: He was reportedly put off by the lowly payment of €128 for each board meeting attended.
"It wasn't easy," said Brandenburg's chief minister Dietmar Woidke, who is credited with having brought him on board. "People are not queuing up [to join]."
From corruption scandals to fire safety systems that didn't work, BER has tarred Germany's reputation internationally as a model of big-project efficiency.
Commentators have said it is increasingly unfitting for the airport to bear the name of Willy Brandt, a German statesman and politician who served as FRG chancellor for 1969 to 1974.
Originally due to open in 2010 a cost of €2.4 billion, BER will replace the capital's Tegel and Schönefeld airports. But the opening date was repeatedly pushed back.
To date, it has cost €5.4 billion, with further costs predicted to be as much as €3 billion.
Initially designed to handle 27 million passengers a year, the hold-ups means that without a third terminal BER will already be undersized when it opens.
According to forecasts, some 31 million people will already fly to Berlin in 2015.
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