Note 3 

Organic fertilizers 
December 2025 

 

  



 

Note 3: Organic fertilizers | Page 1 of 7 CGIAR 

Note 3: Organic fertilizers 

Summary 

Type of nature loss this practice addresses 
✓ Pollution 
✓ Land use change 
✓ Soil degradation 
✓ Invasive Species 

Type of agriculture this practice is most relevant for 
✓ Smallholder farms on forest frontiers  
✓ Agrochemical intensive monoculture  
✓ Water extractive farming 
✓ Intensive livestock systems 

 

Investment bundle 

Organic fertilizers are a key element of organic farming systems. Their application, bundled with other building 

blocks of organic agriculture, such as biocontrol and integrated manure management, enhances ecological 

and economic outcomes. 

Introduction 

Fertilization is a crucial aspect of soil management aimed at regulating the nutrient cycle and 
availability and supporting plant growth and increasing productivity. It involves the application 
of nutrients, either to the soil [1] or to plant foliage [2] to replenish optimal content in the soil 
and, ultimately, in the plants. Fertilization has always been an integral part of agricultural 
production, and its origins can be traced back to around 8000 BCE [3]. Over time the use of 
fertilizers has evolved, and application rates have significantly increased thanks to industrial 
processes [4] that enabled the production of low-priced and accessible synthetic fertilizers. 
Figure 1 shows the extent of the worldwide use of nitrogen-based fertilizers, the most typical 
nutrient applied in agriculture as it is often a yield-limiting nutrient [5], [6]. 



 

CGIAR Note 3: Organic fertilizers | Page 2 of 7 

Figure 1.  Nitrogen fertilizer use worldwide  

Sources: Nitrogen amount and Cropland area: FAOSTAT; Administrative boundaries: World Administrative 
Boundaries - Countries and Territories — Opendatasoft 

 

Despite the importance of fertilizers for increasing crop yields, their use has raised concerns 
about environmental pollution which can lead to biodiversity losses, and potential health risks 
associated with chemical residues. Adequate fertilization requires careful consideration of the 
nutrient balance, timing, and application methods to minimize adverse effects. Otherwise, 
excessive use of synthetic (industry-made) fertilizers can cause leaching and surface runoff, 
leading to the contamination of groundwater and surface water with nitrates and phosphates 
[5], [6], [7]. This may result in eutrophication which reduces biodiversity in water bodies. Soil 
physical and microbial properties are also affected. Overuse of fertilizers causes the 
formation and accumulation of mineral salts, leading to soil compaction and degradation in 
the long term [8]. The massive use of ammonia-based fertilizers causes air pollution due to 
toxic gas emissions [9], [10], [11]. Potential human health risks are also a concern. Direct 
contact or inhalation of fertilizers during application can cause skin and respiratory irritations 
[12], [13]. Finally, the fertilizer industry contributes to the increase of CO2 emissions, since 
the well-established Haber-Bosch industrial process [14] which used to synthesize ammonia 
consumes energy and is responsible for 1.2% of the global anthropogenic CO2 emissions 
[15]. 

Organic fertilizers emerge as a promising solution to these problems, offering a more 
environmentally sustainable approach to crop fertilization. Organic fertilizers contain organic 
materials derived from natural sources and provide the nutrients necessary for plants to 
grow. Common types of organic fertilizers used in agriculture are compost, manure, and 
biofertilizers. Compost is made from decomposing and stabilizing different organic 
substrates, like crop residue and household waste. Animal manure is a traditional organic 
fertilizer rich in nutrients like nitrogen, phosphorus, and potassium. Biofertilizers contain 

https://www.fao.org/faostat/en/#data/RFN
https://public.opendatasoft.com/explore/dataset/world-administrative-boundaries/information/
https://public.opendatasoft.com/explore/dataset/world-administrative-boundaries/information/


 

Note 3: Organic fertilizers | Page 3 of 7 CGIAR 

beneficial microorganisms, such as nitrogen-fixing bacteria and mycorrhizal fungi, that 
enhance nutrient availability and promote plant growth. 

Pathways to Reduced Nature Loss 

Assessment of impacts 

The paragraphs below describe the pathways through which the use of organic fertilizers can 
affect biodiversity and the subsequent pathways through which it impacts ecosystem 
services that support agriculture. These pathways are summarized in Figure 2. 

 

Figure 2. Pathways through which organic fertilizers contribute to reduced nature losses 

Source: Authors 

Like their synthetic counterparts, the first aim of organic fertilizers is to replenish the soil with 
the essential nutrients needed for plants to grow. Hence, they primarily contribute to plant 
growth and health and crop productivity [16], [17]. Research shows that when organic 
fertilizers are correctly used, their impact on crop yields can be similar to that of synthetic 
fertilizers [18].  

Organic fertilizers enhance soil biodiversity by providing a diverse range of nutrients that 
support microbial growth, leading to a richer and more balanced microbial fauna. This 
increase in microbial diversity promotes competition with soil-borne pathogens and leads to 
their possible supersession. Increased microbial activity also facilitates nutrient cycling, 
which leads to healthier soils and reduced pr that contribute to stronger plant growth and 



 

CGIAR Note 3: Organic fertilizers | Page 4 of 7 

reduced stress, indirectly aiding in pest control. The overall result is a more resilient soil 
ecosystem that enhances both disease resistance and natural pest suppression.  

Replacing synthetic fertilizers with organic ones can also be highly beneficial to soil quality; 
organic fertilizers increase soil organic matter can prevent soil degradation and groundwater 
pollution by avoiding salinization and possible nutrient leaching and runoff [19]. They can 
also work as soil amendments, improving soil structure [20], [21] and increasing its water 
retention [22] and organic matter content. This, in turn, generates additional benefits, 
including increased soil carbon storage [23], which can help reduce atmospheric CO2 levels 
and mitigate climate change [24]. Finally, replacing synthetic fertilizers with organic ones has 
even been reported to increase the quality of the agricultural produce in terms of protein and 
various nutrients for human health [25]. 

A relevant aspect concerning the socio-environmental benefits of organic fertilization is the 
potential use of biological wastes to produce valuable fertilizers [26]. For this purpose, a 
variety of by-products of agricultural, industrial, or municipal activities can be used, like food 
losses, crop residues, and animal manure. These organic substances can be diverted from 
landfills or waste and transformed into valuable fertilizers through processes like composting 
[27], anaerobic digestion [28], or vermicomposting [29]. This process of upcycling not only 
produces nutrient-rich fertilizers for agriculture, but also minimizes the environmental burden 
of waste management. This efficient use of resources aimed at waste reduction and 
upcycling is entirely in line with the principles of the circular economy [26]. 

Barriers to adoption  

Widespread use of organic fertilization is limited by several factors. First, synthetic fertilizers 
are cheaper per unit of nutrient Given that farmers may refuse to give up on synthetic 
fertilizers if the alternative does not have a similar nutrient content [30], organic fertilizers can 
be economically inconvenient. Thus, their adoption can be limited, unless farmers prioritize 
environmental benefits over economic performance, or organic fertilizer use is incentivized or 
imposed by policy. An example is the European Union’s Common Agricultural Policy that has 
set a 25% target for organic land across member States. Since organic fertilization is 
intrinsically linked to organic farming, promoting organic fertilizers as part of an organic 
certification scheme will result in higher crop prices and can provide the necessary economic 
incentive for wider adoption of the practice. By the same token, the same biophysical, 
institutional, and market factors that help promote or hinder the expansion of organic 
agriculture will equally affect use of all related organic inputs. These factors differ between 
developing and developed countries. Hence, labor availability and the existence of a well-
established market drive organic farming in the United States [31], whereas farm size and 
farmers’ awareness and education level are the most important drivers for Nigeria [32], [33].  

Further barriers to adoption of organic fertilizers are connected to farmers' behavior, 
perceptions, and social and educational background. For example, organic fertilizers 
produced from waste can be perceived negatively by farmers who are worried about foul 
odors [33] and possible soil contamination [34]. Many studies stress the need to educate 
farmers and increase their awareness about the benefits of organic fertilizers [35], however, 
the impact of farmer education level on their adoption appears ambiguous. While larger 
households in Africa, led by more educated farmers, have been found to be more likely to 
adopt organic fertilizers [36], opposite findings have been reported for South Asia [37]. 
Furthermore, the labor-intensive nature of applying organic fertilizers (e.g., manure) has 
been found to be an important adoption constraint particularly for young and educated 
farmers [35]. Organic fertilization has been found to exert a more significant impact on 
women's labor demand than men [36]. This suggests that increasing the adoption of organic 
fertilizers may call for gender-oriented policies that lead to a more equal distribution of labor 
within the household.  



 

Note 3: Organic fertilizers | Page 5 of 7 CGIAR 

Finally, for countries that import most of their synthetic fertilizers, and are thus subject to high 
world prices (e.g., due to the Ukraine-Russia war), organic fertilizers which are locally 
produced represent a promising alternative [38]. However, challenges such as biomass 
shortages, low animal production, inadequate or costly means of transportation and storage 
can hinder the availability and distribution of manure, even where it is needed most [36], [39].   

Conclusions 

Overall, the use of organic fertilizers represents a key practice for addressing environmental 
and human health concerns stemming from the overuse of synthetic fertilizers. By adopting 
organic fertilization, farmers can contribute to building a more resilient, equitable, and 
environmentally sustainable food system. Policies, incentives, and other mechanisms are 
needed to promote the use of organic fertilizers. The close relationship between organic 
fertilizers and organic agriculture suggests that promoting the practice requires its bundling 
with other practices typically found in organic farming systems, like manure management and 
biocontrol. As markets evolve, there are many opportunities for smallholder farmers—who in 
any case use limited amounts of synthetic fertilizers—to take advantage of the demand for 
organic products. The increasing demand for organic product may be leveraged by African 
countries, where the majority of organic farmers are not certified and sell their organic 
produce informally. Currently, only 0.2% of land is organic certified. Fostering access to 
organic certification may enhance farm development, opening up new markets for selling 
produce. 

References and Further Reading 

[1] C. D. Sutton, “Book Review: Fertilizers and Fertilization. Introduction and Practical Guide to Crop 
Fertilization.,” Outlook Agric, vol. 12, no. 2, 1983, doi: 10.1177/003072708301200220. 

[2] N. K. Fageria, M. P. B. Filho, A. Moreira, and C. M. Guimarães, “Foliar fertilization of crop plants,” J Plant 
Nutr, vol. 32, no. 6, 2009, doi: 10.1080/01904160902872826. 

[3] A. Bogaard, “‘Garden agriculture’ and the nature of early farming in Europe and the Near East,” 2005. doi: 
10.1080/00438240500094572. 

[4] J. Paull, “A century of synthetic fertilizer: 1909-2009,” Elementals: Journal of Bio-Dynamics Tasmania, no. 
94, 2009. 

[5] M. N. Khan, M. Mobin, Z. K. Abbas, and S. A. Alamri, “Fertilizers and their contaminants in soils, surface 
and groundwater,” in Encyclopedia of the Anthropocene, vol. 1–5, 2017. doi: 10.1016/B978-0-12-809665-
9.09888-8. 

[6] A. L. Srivastav, “Chemical fertilizers and pesticides: role in groundwater contamination,” in Agrochemicals 
Detection, Treatment and Remediation: Pesticides and Chemical Fertilizers, 2020. doi: 10.1016/B978-0-
08-103017-2.00006-4. 

[7] Bijay-Singh and E. Craswell, “Fertilizers and nitrate pollution of surface and ground water: an increasingly 
pervasive global problem,” 2021. doi: 10.1007/s42452-021-04521-8. 

[8] J. Massah and B. Azadegan, “Effect of chemical fertilizers on soil compaction and degradation,” AMA, 
Agricultural Mechanization in Asia, Africa and Latin America, vol. 47, no. 1, 2016. 

[9] S. Gyldenkærne, C. A. Skjøth, O. Hertel, and T. Ellermann, “A dynamical ammonia emission 
parameterization for use in air pollution models,” Journal of Geophysical Research Atmospheres, vol. 110, 
no. 7, 2005, doi: 10.1029/2004JD005459. 

[10] Z. Klimont and C. Brink, “Modelling of emissions of air pollutants and greenhouse gases from agricultural 
sources in Europe,” Interim Report IR-04-048, no. September, 2004. 

[11] S. Bittman, J. R. Brook, A. Bleeker, and T. W. Bruulsema, “Air quality, health effects and management of 
ammonia emissions from fertilizers,” in Air Quality Management: Canadian Perspectives on a Global Issue, 
vol. 9789400775572, 2013. doi: 10.1007/978-94-007-7557-2_12. 

[12] M. G. Ng, E. Stjernberg, M. Koehoorn, P. A. Demers, M. Winters, and H. W. Davies, “Fertilizer use and 
self-reported respiratory and dermal symptoms among tree planters,” J Occup Environ Hyg, vol. 10, no. 1, 
2013, doi: 10.1080/15459624.2012.740994. 

[13] T. Nganchamung, M. G. Robson, and W. Siriwong, “Chemical Fertilizer Use and Acute Health Effects 
Among Chili Farmers in Ubon Ratchathani Province, Thailand,” J Health Res, vol. 31, no. 6, 2017. 

[14] R. Lan, J. T. S. Irvine, and S. Tao, “Ammonia and related chemicals as potential indirect hydrogen storage 
materials,” 2012. doi: 10.1016/j.ijhydene.2011.10.004. 

[15] C. Smith, A. K. Hill, and L. Torrente-Murciano, “Current and future role of Haber-Bosch ammonia in a 
carbon-free energy landscape,” Energy Environ Sci, vol. 13, no. 2, 2020, doi: 10.1039/c9ee02873k. 



 

CGIAR Note 3: Organic fertilizers | Page 6 of 7 

[16] A. A. Ahmad et al., “Use of Organic Fertilizers to Enhance Soil Fertility, Plant Growth, and Yield in a Tropical 
Environment,” in Organic Fertilizers - From Basic Concepts to Applied Outcomes, 2016. doi: 
10.5772/62529. 

[17] C. Gao, A. M. El-Sawah, D. F. Ismail Ali, Y. A. Hamoud, H. Shaghaleh, and M. S. Sheteiwy, “The integration 
of bio and organic fertilizers improve plant growth, grain yield, quality and metabolism of hybrid maize (Zea 
mays L.),” Agronomy, vol. 10, no. 3, 2020, doi: 10.3390/agronomy10030319. 

[18] Q. Tang, C. Ti, L. Xia, Y. Xia, Z. Wei, and X. Yan, “Ecosystem services of partial organic substitution for 
chemical fertilizer in a peri-urban zone in China,” J Clean Prod, vol. 224, 2019, doi: 
10.1016/j.jclepro.2019.03.201. 

[19] S. Savci, “Investigation of Effect of Chemical Fertilizers on Environment,” APCBEE Procedia, vol. 1, 2012, 
doi: 10.1016/j.apcbee.2012.03.047. 

[20] Shepherd M.A.*, R. Harrison, and J. Webb, “Managing soil organic matter – implications for soil structure 
on organic farms,” Soil Use Manag, vol. 18, no. 3, 2002, doi: 10.1079/sum2002134. 

[21] J. D. S. Lekfeldt, C. Kjaergaard, and J. Magid, “Long‐term Effects of Organic Waste Fertilizers on Soil 
Structure, Tracer Transport, and Leaching of Colloids,” J Environ Qual, vol. 46, no. 4, 2017, doi: 
10.2134/jeq2016.11.0457. 

[22] R. Ahmad, M. Arshad, A. Khalid, and Z. A. Zahir, “Effectiveness of organic-/bio-fertilizer supplemented with 
chemical fertilizers for improving soil water retention, aggregate stability, growth and nutrient uptake of 
Maize (Zea mays L.),” Journal of Sustainable Agriculture, vol. 31, no. 4, 2008, doi: 
10.1300/J064v31n04_05. 

[23] A. Bationo and J. O. Fening, “Soil organic carbon and proper fertilizer recommendation,” in Improving the 
Profitability, Sustainability and Efficiency of Nutrients Through Site Specific Fertilizer Recommendations in 
West Africa Agro-Ecosystems, vol. 1, 2018. doi: 10.1007/978-3-319-58789-9_1. 

[24] B. C. Ball, B. C. Ball, I. P. McTaggart, and A. Scott, “Mitigation of greenhouse gas emissions from soil under 
silage production by use of organic manures or slow-release fertilizer,” Soil Use Manag, vol. 20, no. 3, 
2004, doi: 10.1079/sum2004257. 

[25] A. Kurniawati, G. Toth, K. Ylivainio, and Z. Toth, “Opportunities and challenges of bio-based fertilizers 
utilization for improving soil health,” 2023. doi: 10.1007/s13165-023-00432-7. 

[26] K. Chojnacka, K. Moustakas, and A. Witek-Krowiak, “Bio-based fertilizers: A practical approach towards 
circular economy,” 2020. doi: 10.1016/j.biortech.2019.122223. 

[27] S. K. Awasthi et al., “Changes in global trends in food waste composting: Research challenges and 
opportunities,” 2020. doi: 10.1016/j.biortech.2019.122555. 

[28] M. Samoraj et al., “The challenges and perspectives for anaerobic digestion of animal waste and fertilizer 
application of the digestate,” Chemosphere, vol. 295, 2022, doi: 10.1016/j.chemosphere.2022.133799. 

[29] H. A. Mupambwa and P. N. S. Mnkeni, “Optimizing the vermicomposting of organic wastes amended with 
inorganic materials for production of nutrient-rich organic fertilizers: a review,” 2018. doi: 10.1007/s11356-
018-1328-4. 

[30] J. Tur-Cardona et al., “Farmers’ reasons to accept bio-based fertilizers: A choice experiment in seven 
different European countries,” J Clean Prod, vol. 197, 2018, doi: 10.1016/j.jclepro.2018.06.172. 

[31] Y. Hou, T. Luo, and J. Hao, “Analysis of Determinants Affecting Organic Production: State Evidence from 
the United States,” Sustainability (Switzerland), vol. 14, no. 1, 2022, doi: 10.3390/su14010503. 

[32] C. O. Ume et al., “Factors influencing smallholder adoption of organic agriculture in Southeast geopolitical 
region of Nigeria,” Front Sustain Food Syst, vol. 7, 2023, doi: 10.3389/fsufs.2023.1173043. 

[33] S. D. C. Case, M. Oelofse, Y. Hou, O. Oenema, and L. S. Jensen, “Farmer perceptions and use of organic 
waste products as fertilisers – A survey study of potential benefits and barriers,” Agric Syst, vol. 151, 2017, 
doi: 10.1016/j.agsy.2016.11.012. 

[34] T. Chen, S. Zhang, and Z. Yuan, “Adoption of solid organic waste composting products: A critical review,” 
J Clean Prod, vol. 272, 2020, doi: 10.1016/j.jclepro.2020.122712. 

[35] D. Qiao, N. Li, L. Cao, D. Zhang, Y. Zheng, and T. Xu, “How Agricultural Extension Services Improve 
Farmers’ Organic Fertilizer Use in China? The Perspective of Neighborhood Effect and Ecological 
Cognition,” Sustainability (Switzerland), vol. 14, no. 12, 2022, doi: 10.3390/su14127166. 

[36] B. E. Daadi and U. Latacz-Lohmann, “Organic Fertilizer Adoption, Household Food Access, and Gender-
Based Farm Labor Use: Empirical Insights from Northern Ghana,” Journal of Agricultural and Applied 
Economics, vol. 53, no. 3, 2021, doi: 10.1017/aae.2021.8. 

[37] J. P. Aryal, T. B. Sapkota, T. J. Krupnik, D. B. Rahut, M. L. Jat, and C. M. Stirling, “Factors affecting farmers’ 
use of organic and inorganic fertilizers in South Asia,” Environmental Science and Pollution Research, vol. 
28, no. 37, 2021, doi: 10.1007/s11356-021-13975-7. 

[38] C. Dimkpa et al., “Fertilizers for food and nutrition security in sub-Saharan Africa: An overview of soil health 
implications,” 2023. doi: 10.3389/fsoil.2023.1123931. 

[39] C. Alewell, B. Ringeval, C. Ballabio, D. A. Robinson, P. Panagos, and P. Borrelli, “Global phosphorus 
shortage will be aggravated by soil erosion,” Nat Commun, vol. 11, no. 1, Dec. 2020, doi: 10.1038/s41467-
020-18326-7. 

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Note 3: Organic fertilizers | Page 7 of 7 CGIAR 

 

 

CGIAR Nature Notes 
This note is part of a series of 15 publications on sustainable agricultural practices to mitigate agriculture-driven nature loss, 
particularly biodiversity. Sustainable agriculture practices are defined as technologies or approaches that mitigate selected 
types of nature loss or enhance positive impacts on nature, are economically viable, support livelihoods, and include diverse 
smallholders. The note examines agricultural drivers of biodiversity loss, impacts on ecosystem services and consequences 
for agriculture.  
 
The 15 notes were developed to support preparation of the World Bank report Rooted: Agriculture Rooted in Biodiversity. 
We are grateful for the financial support of the World Bank Group in preparing this note. The World Bank Group is not 
responsible for the content or accuracy of this note. The work was supported by and benefited from the CGIAR Nature-
Positive Solutions Initiative and Multifunctional Landscapes Science Program. 
 
Suggested citation: Antonio Paparella, Athanasios Petsakos, Kristin Davis, Chun Song, Lorenzo Berti, and Eleonora De 
Falcis. 2025. Organic fertilizers. Note 3. Sustainable Management Practices to Mitigate Agriculture Driven Nature Loss. 
International Food Policy Research Institute and the Alliance for Bioversity International and CIAT. 
 

 

 

https://www.worldbank.org/en/topic/agriculture/publication/agriculture-rooted-in-biodiversity