The Manitoba Crop Diversification Centre's headquarters is its Carberry site. It also operates satellite sites at Portage la Prairie and Winkler. The MCDC sites are strategically located in areas of Manitoba with high-value crop production potential (including irrigation) and a range of representative soils. The headquarters of MCDC at Carberry officially opened on August 4th, 1994. The headquarters at Carberry, and the Portage and Winkler satellite sites are managed and operated by MCDC staff. The Roblin site is operated by the Parkland Crop Diversification Foundation and the Melita site by the Souris Valley Irrigators.

The Carberry site is located on a half-section of excellent agricultural land ( mostly Wellwood and Ramada clay loam and loam) at the junction of Highways #1 and 5. Buildings include an office-lab classroom complex, a building for sample processing, shop work and machinery storage, a chemical storage building, and grain bins. Equipment for most operations is owned, while some field and research operations are contracted out or conducted by project cooperators. An advanced irrigation system has been installed which permits irrigation of approximately 70 ha of land, using three pivot irrigators and two linear-move systems well-adapted to meet the needs of irrigation research trials. This capability is unique to MCDC in Manitoba, so the Centre attracts most research in the province requiring good irrigation control.

The Portage la Prairie site was previously an Agriculture and Agri-Food Canada Research Branch sub-station. Two linear-move field irrigators and an irrigation water supply system were set up to irrigate much of the land base of over one-quarter section, mostly good quality clay loam.

The Winkler site consists of approximately 16 ha of sandy loam land, mostly irrigable by linear- move field irrigator. There are no buildings or full-time staff on-site. Most field and plot operations are carried out by seasonal staff from the Portage la Prairie site, while other services are contracted out locally.

The majority of the Centre's assets at the main site, including land, building and irrigation equipment, are owned by MHPEC.

Development funds for the Centre were provided by Canada through Western Economic Diversification and Prairie Farm Rehabilitation Administration (PFRA); the Manitoba government through the Sustainable Development Innovations Fund (SDIF); and jointly by both levels of government.