Contrary to the seed collections, the apple trees need yearly maintenance. The CGN orchard is situated at the Experimental Station Randwijk and surrounded by other experimental orchards. The same maintenance regime is applied to the CGN orchard as to the others.

This means pruning in winter (February), weekly chemical control against scab during the growing season, chemical control against aphids and after harvest, 2-3 times spraying with lime against infection of apple canker. When it is very dry, the trees are watered.

Because apple trees are vulnerable to Apple Canker (Nectria galligena), they are checked and treated during pruning. Trees are treated by cutting away infected wood. When more than three large lesions are present which cannot be treated anymore, the tree will be removed. From the remaining healthy trees, five scions are cut. These scions are sent to a commercial tree nursery. This company will graft the scions on M.9 rootstock and grow the trees for two year. After two years the new trees are sent back and planted on the spot of the removed tree.

Within the European Union it is obligatory to check for two quarantine diseases when apple material (trees, scions) is distributed. Therefore the orchard is checked twice a year for Fire Blight (Erwinia amylovora) and Apple Proliferation disease by the Netherlands Inspection Service for Horticulture (NAKtuinbouw). The material can be distributed in the European Union, accompanied by a plant passport.

Since 2017, part of the collection has been planted on the Campus of Wageningen University & Research and can be considered as a safety duplicate. One-hundred and ten accessions in a so called time-line, show apple cultivation from the past until present. Some wild species, about 20 varieties, are grafted on a high trunk and strong rootstocks and a small orchard with 80 old varieties on weak rootstock are grown at the Campus.