The company was chosen out of an international field of top Microsoft partners as delivering market-leading customer solutions built on Microsoft technology.
Anglia's managing director David Hurley said: "The award is a significant tribute to the skill, dedication and innovation applied by our people in helping our customers improve their business."
The Microsoft Dynamics NAV Partner of the Year Award honours partners who have exhibited excellence in providing innovative and unique solutions based on Microsoft Dynamics NAV.
Doug Kennedy, Microsoft's vice president of Dynamics Partners, said: "LINKFresh provides an end-to-end process based on the Microsoft stack that addresses the needs of the food manufacturing sector. LINKFresh helps customers reduce inefficiencies, optimise resources, refine processes and ultimately drive down costs."
Anglia's customers include Branston, AV Produce, Lincolnshire Field Products, Marshalls and Produce World.