EU organic crop production standards prohibit or restrict the use of many external inputs that are widely used in conventional cereal production to ensure high grain yields and processing quality [1]. Specifically, organic farming standards prohibit the use of (a) mineral nitrogen (N), potassium chloride (KCl) and water-soluble phosphorus (P) fertilizers and (b) synthetic chemical crop protection products (including insecticides, acaricides, fungicides, herbicides, plant growth regulators and soil disinfection chemicals) [1].

Fertilization regimes in organic farming systems are largely based on regular inputs of organic fertilizers (e.g., manure and composts) and the use of legume crops in the rotation (to increase N levels and balance N:P ratios in the soil). However, restricted use of raw phosphate, potassium sulphate and mineral micronutrient fertilizers is permitted if shown to be necessary (by soil or plant analysis) to maintain soil fertility [1]. It is important to point out that EU environmental legislation also limits the amount of manure (the main N fertilizer available to organic farmers) that farmers can apply to their crops ^[2][3][2,3]. For example, in nitrate sensitive zones, the total N input from manure is limited to the equivalent of 170 kg N/ha/year, although inputs to specific crops can be higher (up to an equivalent of 250 kg N/ha) if this is balanced out by lower inputs to other crops in the rotation ^[2][3][2,3]. Both plant available and total N inputs from organic fertilizers to organic crops are therefore usually lower compared with the inputs of mineral N fertilizers to the same crops in conventional production systems in Europe ^{[1][4][5][6][7][8][9]}[1,4,5,6,7,8,9].

It is also important to consider that N supply/availability profiles over the growing season differ considerably between mineral N and organic fertilizers such as animal and green manures ^{[1][4][5][6][7][8][9][10]}[1,4,5,6,7,8,9,10]. The NH₄⁺-N_, NO₃⁻-N and urea-N in mineral N fertilizer products is immediately plant available and after application the concentration of plant available N fertilizer decreases steadily due to plant uptake, metabolism by soil micro-organisms and N losses (e.g., nitrate leaching, run-off or denitrification). In contrast, only a small proportion of total N in organic fertilizers is plant available NH₄⁺ or NO₃⁻, while a large proportion is present as organic N forms which only become available for plant uptake after mineralization in the soil ^{[1][4][5][6][7][8][9][10]}[1,4,5,6,7,8,9,10]. Numerous studies have shown that only ~50% of N applied from green and animal manures becomes available to the crop planted immediately after application, although the amount of residual N that is available to subsequent crops is higher from manure when compared with mineral N fertilizer inputs ^{[1][4][5][6][7][8][9][10]}[1,4,5,6,7,8,9,10]. N availability patterns from organic fertilizers are therefore less predictable and determined by parameters such as soil microbial activity and environmental parameters (soil organic matter content, temperature and soil matric potential) that affect mineralization processes ^{[6][7][8][10][11]}[6,7,8,10,11].

The agronomic protocols used for organic wheat production in Northern and Southern Europe differ substantially from those used in intensive conventional production in terms of (i) tillage, (ii) rotational design, (iii) fertilization regimes and (iv) crop protection practices ^{[4][6][7][9][12][13][14]}[4,6,7,9,36,37,38].

Reduced tillage is now widely used in conventional arable farming systems, while many organic farmers continue moldboard ploughing before planting of wheat crops primarily to (i) incorporate green and animal manures, (ii) control weeds ^{[15][16][17][18]}[39,40,41,42] and (iii) reduce disease inoculum through the burial of trash and stubble. Mechanical weed control based on tine weeders and inter-row weeding systems is also more widely and frequently used in organic production systems, with herbicides being the main method of weed management in conventional production systems ^{[1][4][6][7][9][19][20][21][22]}[1,4,6,7,9,23,43,44,45].

Long-term field experiments in both Northern Europe and North America suggest that, overall, the efficacy of mechanical weed control protocols used in organic farming is lower than the herbicide-based protocols used in conventional farming ^[18][19][20][23,42,43]. Both the lower efficacy and crop damage associated with mechanical weed control protocols may have significant negative effects on wheat yields and quality in organic farming ^[22][45].

Conventional wheat production is primarily based on stockless, short, cereal-dominated rotations and only farms which continue to have livestock regularly include pure grass or mixed grass–legume leys in the rotation ^[1][23][24][1,46,47]. In addition, many conventional arable rotations include (i) only one break crop (e.g., oilseed rape in many regions of Northern Europe) and (ii) second wheat crops (wheat grown after wheat), especially when wheat prices are high. In addition, when maize is included in the rotation, wheat may be established after maize crops in conventional arable rotations, although it increases the risk of Fusarium disease and mycotoxin contamination in the harvested grain ^[1][23][24][1,46,47].

In contrast, a large proportion of organic wheat is produced in mixed farming systems which usually have a 2–3-year pure legume or mixed grass/legume sward in the rotation ^[1][23][24][1,46,47]. Where wheat is produced on stockless organic farms, rotations usually include a 2–4-year legume or grass/legume ley phase for fertility building. In organic systems, wheat is often grown immediately after fertility building leys to achieve higher yields and/or to achieve the minimum bread-making quality standards (e.g., protein concentrations of 13% in the UK) set by processors for premium prices ^[4][7][13][4,7,37]. Overall, organic rotations in Europe tend to be more diverse and may include field vegetables, potatoes and grain legumes; wheat is rarely grown following wheat or maize in the rotation (due to increasing the risk of pest and disease damage) and oilseed rape is less frequently used when compared with conventional arable rotations (^{[1][7][23][24]}[1,7,46,47]).

In the main wheat growing region of Northern Europe, conventional common wheat crops (Triticum aestivum L.) receive mineral N fertilizer inputs often in excess of 200 kg N/ha, although lower N inputs (~100 kg/ha) are usually applied to spelt wheat (Triticum spelta L.) ^{[4][9][12][13][14]}[4,9,36,37,38]. Substantial P (up to 110 kg P₂O₅/ha) and K (up to 150 kg/ha K₂O) inputs are also applied to wheat crops, but input levels vary widely depending on the residual soil P and K levels; many conventional farmers use soil analysis and management information (e.g., soil type and previous crop and straw incorporation or removal) for decision making on P and K inputs ^[12][36].

It is more difficult to estimate the mean total and available N inputs to organic wheat crops, since (i) residual N input from preceding legume leys is both highly variable and difficult to measure and (ii) both total and available N in animal manure can vary greatly depending on manure type, processing and storage methods ^{[1][9][12][13]}[1,9,36,37]. However, because (a) only a proportion (often <50%) of total N from both green and animal manure is considered to be available to the first crop planted after manure inputs and (b) because environmental legislation limits input of animal manure to 170 kg N/ha, the amount of N available to organic cereal crops is significantly lower when compared to mineral N inputs in conventional systems. While mineral N fertilizers are prohibited, organic farmers are able to supplement P and K inputs with permitted mineral P (finely ground rock phosphate) and K (K₂SO₄) fertilizers [1]. As a result, nitrogen is thought to be the primary growth and yield limiting nutrient in most organic production systems ^[25][48].

Conventional crop protection protocols rely on the intensive use of synthetic chemical crop protection inputs. For example, according to the UK Pesticide Usage Survey in 2016, UK winter wheat crops on average received 3.6 fungicide, 2 plant growth regulator and 3 herbicide treatments, plus 1 insecticide treatment (https://secure.fera.defra.gov.uk/pusstats/surveys/index.cfm; accessed 26 February 2023). However, the combinations and amounts of pesticides differ considerably throughout Europe, depending on (a) climatic conditions, (b) regional pest, disease and weed pressure and (c) levels of restriction from national environmental legislation ^[26][27][49,50].

In contrast, the use of synthetic chemical pesticides is prohibited in organic farming systems and crop protection is based on cultural and mechanical control, although some organic farmers use (i) plant extract (e.g., tillekur) based fungicides as seed treatments for the control of seed-borne diseases, (ii) sulfur fungicides for foliar disease control and/or (iii) plant extracts (e.g., pyrethrum) and/or microbial fermentation (e.g., Spinosad) based insecticides for pest control in cereals [1].

Results from long-term, factorial field experiments have demonstrated that the severity and ranking of crop protection challenges, in terms of economic impact and relative need for intervention, differ considerably between conventional and organic wheat production systems. For example, in Northern Europe the severity of lodging and biotrophic diseases such as mildew and rust in manure-fertilized organic crops was (i) significantly lower than in mineral NPK-fertilized crops grown without fungicide/growth regulator treatment and (ii) below the threshold at which fungicide/growth regulator applications would become economically viable in conventional farming ^[4][6][7][4,6,7]. In addition, a recent literature review by Bernhoft et al. ^[28][51] concluded that, overall, the risk of Fusarium head blight and mycotoxin contamination of wheat grain is lower in organic compared with conventional production systems. They describe a range of agronomic factors linked to an increased risk of Fusarium infection and mycotoxin levels in conventional production. Interestingly, risk factors in conventional systems include (i) minimum tillage, (ii) short rotations, especially growing wheat after wheat or maize, (iii) high N fertilizer inputs, and (iv) the use of certain types of fungicide (e.g., strobilurins) and the growth regulator chlormequat, which is used to reduce stem length and the risk of lodging in wheat ^[28][51].

In contrast, when leaf blotch (caused by Septoria tritici) severity was compared in a modern UK short straw variety (Malacca), disease severity was similar in both organic and mineral NPK-fertilized crops grown without fungicide/growth regulator treatment [4]. Disease severity in both systems was above the level at which fungicide treatments are economically viable in conventional cereal production [4].