Preben Damgaard, vice-president for Europe, Middle East and Africa (EMEA) operations at Microsoft's Business Solutions unit, will leave Microsoft at the end of June.
Damgaard plans to spend more time with his family and pursue other personal and professional interests after spending 20 years building a software business, Microsoft said.
Damgaard joined Microsoft through the company's takeover of Navision in July last year. He was president and one of two chief executive officers (CEOs) at Navision and now oversees Microsoft's largest product development centre outside the US in Vedbaek, Denmark, the old Navision headquarters.
Prior to joining Navision, he headed software company, Damgaard, which he founded in 1983 with his brother and merged with Navision in December 2000.
The remaining founders of Navision - including Jesper Balser, Erik Damgaard, Torben Wind and Peter Bang - are staying with Microsoft, the company said.
Microsoft Business Solutions makes software to help small and medium-sized businesses manage supply chains, finances and customer relationships.
MS entered the business application market when it bought Great Plains Software in late 2000 and expanded that with the Navision takeover.
Chief competitors include SAP, Oracle and Siebel Systems.