In Mustang's ASX market release, the company said it "emphasises" Jordaan's decision to resign was his, and that the board "reluctantly accepted his resignation" as an executive.
He will remain as a non-executive director.
Mustang is now looking for a new MD.
Mustang had been expected to generate revenue in the order of A$10-20 million (US$7.6- 15.3 million) from the maiden sale of its rubies from Montepuez in Mozambique, however, the rubies it sold brought in only $713,456.
The result saw investor interest in the stock collapse, with shares that were changing hands at 16c late last month now valued at less than one-quarter of that amount.
The company has since announced a new ruby strategy and accelerated its graphite exploration plans.
Shares in Mustang were down 2.5% in midday trade, capitalising the company at $30 million.