The German manufacturer announced at the end of February it would reduce its forecast for the 2017 and 2018 financial years after a review of its budgets.
The firm said the fall in revenues was due to "reduced expectations for businesses in certain core markets".
Shares in the company fell around 35% after it announced revenues in 2017 should be €3.1-€3.3 billion, and €3.4-3.6 billion in 2018, down from an expected €4.2 billion.
Nordex share price fell from €19.72/share prior to the forecast warning to a low of €13.10/share and has not shown any signs of recovery since, trading on 20 March at €13.78/share.
On his resignation, Krogsgaard said: "Nordex is fundamentally stronger than ever, but our credibility has suffered as a consequence of the outlook, and this follows a period, where our handling of communication matters has been criticised.
"This is, ultimately, my responsibility, and I have therefore proposed to the supervisory board that I am released from my contract on mutually acceptable terms in the company's best interest."
Krogsgaard was appointed CEO in June 2015, following the departure of Jurgen Zeschky. Prior to this role, Krogsgaard was Nordex chief sales officer from 2010.
Nordex board chairman Wolfgang Ziebart said: "During Lars' tenure our company has more than tripled in size at steadily improving margins, and we have become a truly global player. This would not have happened without Lars' vision and energy.
"I regret Lars' departure, but the full supervisory board respects his decision to do what is considered to be in the best interest of the company."
Jose Luis Blanco will replace Krogsgaard from 31 March 2017. He is currently the company chief operations officer (COO) and deputy CEO, following Nordex's acquisition of Spanish manufacuturer Acciona Wind Power in 2016, where Blanco was CEO.
Blanco also previously spent a number of years at Gamesa, holding several roles.