Coffee LATAM baseline: Why emission factor baselines matter and what it means for your Scope 3 reporting

Food companies sourcing coffee need credible emission factors to calculate their Scope 3 footprint. A new regional baseline study, the Latin American Coffee Carbon Footprint Baseline Study published by Conservation International under the Sustainable Coffee Challenge, provides exactly that for five major origins. In this piece we cover what the study found, where emissions actually come from, and what it means for your Scope 3 reporting.

What is a baseline, exactly

A baseline is a reference point that tells you the average greenhouse gas emissions associated with producing a specific product, in a specific place, under typical conditions. Think of it as the starting line: before you can measure reduction, you need to know where you're starting from.

In agriculture, baselines are usually expressed as an emission intensity: how many kilograms of CO₂-equivalent are emitted per kilogram of product. For coffee, that means kg CO₂-eq per kg of green bean equivalent (GBE), which is the standardized unit for coffee. A good baseline is statistically representative, methodologically transparent, and built on primary data from real farms.

Why does this matter? And what are baselines actually used for?

For food and beverage companies, you need baselines to calculate emission reductions for your Scope 3 accounting. Without a credible baseline, you are either guessing, relying on generic industry averages, or skipping this category entirely.

Baselines are also important for:

• Target setting: Science-based targets require a baseline year to calculate reductions against.
  
  
• Supplier engagement: Baselines help you identify which origins or supply chains carry the most emissions per tonne.
  
  
• Emission hotspot identification: They show where emissions are concentrated so you can take action.
  
  
• Benchmarking over time: Repeated studies track whether the sector is actually decarbonizing.

This is exactly the field Proba works in, and why this report is interesting and worthwhile to our audience. When food companies want to reduce Scope 3 emissions from fertilizer use in their agricultural supply chains, the starting point is understanding the amount of emissions you’re currently working with.

Proba's methodologies and certification are designed to give those numbers credibility: verified, traceable, and usable in corporate GHG inventories.

How did they study approach this?

The Latin America Coffee Carbon Footprint Baseline Study was launched under the Sustainable Coffee Challenge, led by Conservation International, and implemented by Meo Carbon Solutions together with Global Risk Assessment Services and 4C Services. Nine major roasters, including Nestlé, Starbucks, JDE Peet's, Lavazza, and Tchibo, governed the study and funded it.

The scope was across Brazil (both Arabica and Robusta), Colombia, Honduras, Mexico, and Peru. Surveying over 3,000 farms and using the The Cool Farm Platform (CFP) perennials module v2.0 for calculation.

The results

Here are the national farm-gate baselines from the primary tool (CFP), expressed in kg CO₂-eq per kg GBE:

Colombia's relatively high footprint reflects intense fertilizer use combined with high crop residue emissions. Mexico's low footprint is driven by lower input intensity across the board. Honduras stands out for its anaerobic residue handling, which drives high methane emissions.

These numbers are national averages. Farm-level variability within each country is substantial. But at the sector level, they are robust enough for benchmarking, target setting, and Scope 3 Category 1 default emission factors.

Where do the emissions actually come from?

1. Fertilizer production and application

Fertilizer is the single largest emission source in almost every country assessed. There are two main emission sources for fertilizer: upstream, from the energy-intensive manufacturing process, and downstream, from direct and indirect nitrous oxide (N₂O) emissions after application. N₂O has a global warming potential 273 times that of carbon dioxide (CO₂), even small nitrogen losses translate into significant climate impact.

Across all countries, synthetic fertilizers dominate: 71% in Brazil Arabica, 96% in Colombia and Honduras, 98% in Brazil Robusta, and 99% in Mexico. Peru is the outlier, with 40% organic fertilizers and the lowest application rates in the study.

Colombia leads on emission intensity from fertilizer at 3.35 kg CO₂-eq per kg GBE. Brazil Arabica sits at 1.90. Mexico and Peru are well below 1.00.

This is where Proba's work is directly relevant. The fertilizer component of a coffee supply chain's Scope 3 footprint depends heavily on which fertilizers are used, how much is applied, and where they were manufactured. When farmers switch to lower-carbon fertilizer technologies, Proba's fertilizer-specific GHG methodologies quantify and certify the resulting emission reduction at farm level, giving food companies verified numbers they can use in their Scope 3 reporting.

2. Fuel and energy use

Fuel and energy is a minor contributor across all origins, accounting for less than 2% of total emissions in most cases. The main driver is diesel consumption for on-farm machinery and processing operations, with electricity use playing a secondary role.

3. Pesticide and herbicide use

Pesticide emissions are negligible in every country assessed, contributing less than 0.2% of total farm-gate emissions across the board. Emissions in this category are calculated based on the life-cycle impacts of pesticide manufacturing rather than application effects.

4. Crop residue management

Crop residues are the second largest emission source in most origins, and the largest in Peru, where they account for 67% of total emissions.

Residue emissions come from two gases: N₂O, produced when nitrogen-rich biomass decomposes aerobically in soil, and CH₄, produced under anaerobic conditions such as heaps, pits, or unmanaged piles of wet pulp. The balance between these two gases varies significantly by country and reflects local management practices.

5. Wastewater

Wastewater contributes marginally in Brazil and Colombia but is more significant in Honduras (4.3% of emissions) and Peru (around 4%). The emissions come entirely from methane produced during anaerobic degradation of organic matter in processing wastewater.

6. Transport

Transport is consistently the smallest or second smallest category across all origins, contributing less than 3% of total farm-gate emissions everywhere. Variability is driven by distance and yield rather than by systemic differences in production. Colombia shows the lowest transport emissions (0.01 kg CO₂-eq per kg GBE) due to centralized collection structures. Brazil Arabica is the highest at 0.07, reflecting longer logistics distances.

The study concludes that transport is not a primary mitigation lever relative to on-farm emission sources.

Using baselines in corporate accounting and sourcing

The study is explicit about how these numbers should and should not be used.

What they are good for:

Companies can use the national baselines as default emission factors for Scope 3 Category 1 (Purchased Goods and Services) reporting, particularly where farm-level primary data is not yet available. They can inform procurement decisions by flagging origins with higher emission intensities, support sector-level target setting, and anchor conversations with suppliers about reduction pathways.

The study specifically recommends using baselines to identify hotspots, design mitigation strategies focused on dominant emission drivers, and progressively replace national averages with supplier-specific data as data maturity improves.

What they are not:

The baselines are not farm-level performance benchmarks, and they should not be used as compliance thresholds or procurement scoring tools. Farm emissions vary significantly within every country, and a national average does not reflect the performance of any individual producer.

The Scope 3 connection:

For food companies with GHG Protocol-aligned reporting, agricultural raw materials like coffee sit in Scope 3 Category 1. The emission factor used to calculate your footprint for a tonne of coffee purchased from Honduras is exactly the kind of number this study provides. If your suppliers are using low-carbon fertilizer technologies, quantified and certified under methodologies like Proba's, that improvement is reportable against the baseline. That is how reduction claims in Scope 3 sourcing go from narrative to number.

The study also notes that future assessments should consider the GHG Protocol's recently released Land Sector and Removals Standard (LSRS), which changes how soil carbon, land use change, and removals are accounted for. Companies building multi-year Scope 3 reduction strategies in agriculture will need to be aware of how emissions are accounted for.

Now what?

Baselines like this one are a starting point, not a finish line. If you're a roaster or trader thinking through what credible Scope 3 reduction actually looks like in your coffee supply chain, we'd be glad to talk through the numbers with you.