Apple scab is the primary fungal disease in apple cultivation affecting entire harvests as well as the following year's production. The damage can occur both in the plant and during storage. In organic farming, scab control is mostly carried out using precautionary measures. Plant protection products are used for direct control before the onset of rain and during spore germination as "scab stop".

Codling moth (Cydia pomonella) is the primary pest in organic fruit growing. It damages apple, pear, quince, rowan, medlar, walnut and kaki. Generations/years vary depending on the soil and climates zones. Several control methods can be applied in organic farming depending on the infection rate, but plant protection products and mating disruption are the most common. Choosing suitable methods may reduce the time for intervention in the field.

Sawflies, such as apple sawfly (Hoplocampa testudinea) and Pear sawfly (H. brevis), are major pests in organic fruit production which can cause massive yield losses. Regulation is possible by only a few measures.

Combining different preventive strategies and direct measures can help to control the pest.

Fertilization of organic fruit orchards strongly relies on authorized external commercial fertilizers leading to nutrient flows from conventional into organic farming systems. The use of alternative fertilizers including legume-based materials and non-contentious external commercial fertilizers, should be based on locally available resourced. An integrated approach is recommended.

The Woolly apple aphid (E. lanigerum) can cause severe damage, especially in organic cultivation; sucking activity causes bark growth, the so-called blood louse canker.

Promoting natural antagonists in organic orchards is a key element in controlling E. lanigerum. Further, the tree growth should be balanced through proper (root) pruning.

Organic fruit orchards are dependent on commercial organic fertilizers derived from intensive conventional animal husbandry. These inputs are contentious and to be phased out. The document proposes as a solution to develop new fertilization strategies based on farm internal resources (e.g., clover based), plant-based sources (e.g., grain legumes as living mulch in the tree row, cover crops).

A BioFruitNet publication - Traditional vigorous seedling rootstocks like Mazzard F 12/1 (Prunus avium L.) and Mahaleb (P. mahaleb L.) typically bear the first crop between the fourth and sixth year and achieve full production between the eighth and twelfth year, leading to delayed returns of investments.

Growing sweet cherry cultivars on the next generations of semi-dwarf and dwarf cherry rootstocks will allow the orchard to produce fruits earlier than using traditional rootstocks.