Brazil stands as the world’s leading coffee producer and exporter, accounting for over one-third of the total global production (CONAB, 2024). With extensive cultivation areas located in southern Brazil, the state of Minas Gerais is responsible for about two-thirds of the Brazilian productivity (Tieghi et al., 2024). The southern and southwestern Brazilian regions offer coffee plantations optimal growing conditions. Indeed, successful C. arabica cultivation in tropical regions is influenced by a combination of environmental and crop management factors. Optimal cultivation occurs under mean annual temperatures of 14–26°C, annual precipitation ranging from 1,000 to 2,700 mm, and a distinct dry season of 1–3 months. These conditions are typically associated with altitudinal ranges of approximately 400–1,200 m above sea level in tropical regions, or 1,000–2,100 m above sea level in equatorial regions (Ahmed et al., 2021). However, those optimal conditions are being increasingly threatened by climate change, which directly affects flowering, fruit ripening, and pest incidence, impacting quality, productivity and price (Ahmed et al., 2021; Faraz et al., 2023).

Besides the natural environmental conditions, coffee´s physiological growth stages are highly dependent on the nutrient availability, being nitrogen (N), phosphorus (P), and potassium (K), the primary macronutrients influencing yield and bean quality. Nitrogen, with optimal range levels varying between 51 mg/kg and 87 mg/kg is especially important for the vegetative growth; Appropriate values of potassium (ranging from 78 and 156 mg/kg) contribute to enhanced bean quality and prevents plant defoliation; Soil phosphorus, with suitable values between 10 and 20 mg/kg is essential to for enhances leaf gas exchange, photosynthesis, and overall growth of young arabica coffee plants, even under water deficit conditions (Rakocevic et al., 2022; Chilito et al., 2025).

The quality of the final product is dependent on the chemical composition of the green beans, rich in bioactive compounds such as phenolic compounds, alkaloids and diterpenes, as well as primary metabolites such as sugars, lipids and amino acids. After roasting, those compounds develop the characteristic flavor, aroma and other sensory attributes, which will give coffee the many different classifications and market value (Várady et al., 2022).

It is well known that the relative concentration of such compounds is dependent on the combination between the genetic background, the geographical origin and environmental growing conditions (Tieghi et al., 2024). However, up to date, no study has evaluated the influence of implemented sustainable agronomic practices with the quality of the final product in terms of chemical profile of the green beans and the corresponding sensory score provided by the roasted beans. Therefore, this study examines the hypothesis that superior coffee quality is associated with production areas where sustainable management practices are applied. It also provides preliminary insights into the relationship between local environmental factors, agricultural management, and coffee biochemistry.

The non-supervised multivariate data analysis (PCA) indicated the feasibility of distinguishing coffees originating from two distinct producing regions based on the concentrations of eight bioactive compounds (four alkaloids and four phenolic compounds) ( Figure 1C ). It is worth noting that the chemical information preserved within the green beans was utilized for this purpose. Roasting transforms the chemical composition of green beans into volatile and non-volatile compounds responsible for the aroma and flavor of a cup of coffee. The main chemical reactions involve the decomposition of sugars, oxidation of lipids, pyrolysis, and the Maillard reaction (Angeloni et al., 2021; Moon et al., 2025). Chlorogenic acid was the most abundant compound quantified in the present study and underwent substantial degradation during roasting (Liao et al., 2022). Its degradation is expected as it is an unstable ester of caffeic acid and quinic acid, easily converted into these two compounds in the roasting process. Subsequent reactions give rise to a variety of volatile compounds, such as phenol, benzoic acid, catechols and their derivatives, as well as non-volatile compounds, including quinic acid epimers and lactone derivatives of chlorogenic acids (Viencz et al., 2023). These compounds collectively contribute to the sensory characteristics of the coffee (Hu et al., 2020). Additionally, a decrease in caffeic acid levels was observed, consistent with previous studies on roasting processes (Alcantara et al., 2025; Rzyska-Szczupak et al., 2025). Trigonelline, the second most abundant compound quantified in this study, also underwent decomposition during roasting. Its degradation generates flavor and aroma desirable products, including furans, pyrazines, alkyl-pyridines, and pyrroles (Toci et al., 2020; Wu et al., 2022). Following the abundance sequence, the caffeine content did not change significantly during roasting. This observation is expected given its well-established stability in the literature (Tarigan et al., 2022). The other evaluated metabolites underwent statistically significant but biologically subtle alterations.

Notably, the chemical constituents measured in the green bean exhibited correlations with altitude, SOM, SOC, and the overall quality of the brewed beverage ( Figure 2A ). These findings offer a chemical rationale for the different cultivation and environmental conditions shown by the two contrasting locations, and their influence on the sensory attributes of the final beverage (coffee after roasting and extraction). Trigonelline, ferulic acid, and p-coumaric acid were the principal chemical constituents responsible for distinguishing the geographical origin of the coffee beans. From those, p-coumaric acid, in addition to all xanthine alkaloids (theobromine, theophylline and caffeine) showed stronger negative correlation with altitude ( Figure 2A ). Interestingly, coffee exhibiting reduced concentrations of these compounds were also associated with higher sensory scores. Higher soil organic matter was associated with lower levels of trigonelline, theophylline, caffeine and ferulic acid. Our observations are consistent with the lower content of caffeine and trigonelline in coffees grown in richest organic matter soil observed by Gebrekidan et al. (2019). Unprecedently, we also report a negative correlation between theophylline and ferulic acid with organic matter in soil. Interestingly, soil organic matter and organic carbon stock correlated positively with coffee quality.Those findings revealed that high-quality coffee beans presented reduced concentrations of xanthine derivatives, in addition to p-coumaric acid. Coffee beans possessing relatively lower amount of those compounds in the green beans were predominantly sourced from elevated regions with soils enriched in organic matter, reinforcing the observation that coffees cultivated at CRV, a farm characterized by higher altitude and higher SOC content, consistently achieved superior sensory score.

From the agricultural practices’ perspective, although SOM content is statistically similar between the two farms, SOC levels are significantly higher in CRV. It is noteworthy to mention that the higher average soil organic carbon (SOC) stock observed in the CRV region ( Figures 1F , 2B ) can be partially attributed to its elevated altitude. Cooler climates at higher altitudes tend to suppress microbial activity, thereby slowing the decomposition rate of soil organic matter (SOM) and enhancing SOC sequestration (Li et al., 2022; Pellikka et al., 2023). Both SOM and SOC play a critical role in improving crop yields and creating favorable soil conditions for coffee cultivation (Sousa et al., 2018; Tassew et al., 2021; Freitas et al., 2024). Besides, the adoption sustainable agricultural management practices at CRV also promotes SOC accumulation through several measures: (i) maintaining vegetation cover interspersed within cultivation areas; (ii) reducing the spacing between rows to increase plant density; (iii) practicing manual harvesting in steep areas to minimize soil compaction; (iv) enhancing the incorporation of plant residues into the soil; and (v) maintaining higher biomass in the cultivated plants. These practices not only increase SOC levels but also improve soil nitrogen (N) retention, thereby reducing the dependence on synthetic fertilizers (Tassew et al., 2021; Yin et al., 2022).

In addition, other agronomic practices employed in CRV may contribute to improved crop quality. These include (i) selective harvesting at optimal ripening stages, (ii) close monitoring of climatic conditions, (iii) annual soil and foliar analyses, (iv) efficient fertilizer application, and (v) proper post-harvest storage of beans (Worku et al., 2018; Alliance for Coffee Excellence, 2023). Collectively, these measures help reduce pest incidence and promote the development of denser, higher-quality beans (Cheng et al., 2016). They also contribute to prolonged fruit ripening and improved soil drainage, resulting in beans enriched with complex sugars, acids, and amino acids that enhance the sensory characteristics of the final beverage (Matiello et al., 2005; Vaast et al., 2006).

Those observations are corroborated by a previous study from Silveira et al. (2016), which concluded that altitude, associated with good agricultural management practices, were the major factors influencing coffee quality in Matas de Minas (Silveira et al., 2016). However, it is important to mention that altitude, temperature and rainfall may not directly impact beverage quality; instead, they can create the best environmental conditions for growing coffee (Gumecindo-Alejo et al., 2021).

It is important to highlight that both regions included in the present study favours the cultivation of C. arabica. However, the suitability of a region for coffee cultivation depends on several factors. Even within the same favourable areas, significant variations arise from microclimates, soil characteristics, and management practices. In our study, the region of Alfenas has lower altitudes and higher temperatures, which accelerates the maturation cycle, and potentially reducing the accumulation of sugars and aromatic compounds (Ramalho et al., 2018). In Conceição do Rio Verde, higher altitudes and cooler climate prolong maturation, allowing for a greater development of flavour complexity, vibrant acidity, and a richer aromatic profile, which are commonly associated to specialty coffees profiles. It is worth noting that the sensory analysis of roasted beans from each farm reflected the chemistry of the original green beans, revealing clear differences in cup quality and in the corresponding aromas and flavors – samples from CRV showing higher sensory score in comparison to samples from ALF. Interestingly, the samples from ALF showed higher variation among the sensory scores in comparison with the samples from CRV ( Figure 1H ). That result may suggest that the higher variation in the sensory score of samples from ALF might be due to the general management practices employed on that farm. Finally, attention should also be drawn to the fact that coffee is a highly demanding crop, and nutrients availability can still alter its physiological development. Hence, the application of appropriate fertilization regimes is important to fulfil the nutritional demands of coffee throughout its vegetative and reproductive stages, supporting optimal photosynthetic performance, and contributing to higher yields and superior bean quality (Li et al., 2023).

The present study identifies a relationship between sustainable management practices, coffee bioactive chemical profile and quality. Although further research is currently ongoing to deepen the understanding, the results suggest that the chemical information preserved within the green beans can be associated with altitude, SOM, SOC, and the overall quality of the final beverage. Notably, while trigonelline, ferulic acid, and p-coumaric acid were the principal chemical constituents responsible for distinguishing the geographical origin of the coffee beans, lower levels of all xanthine alkaloids in addition to ferulic and p-coumaric acid were associated to higher quality and higher altitudes, providing a chemical rationale for the observed variations in coffee quality across different farms and production regions.

A limitation of this study is the relatively small sample size, which may affect statistical power and is characteristic of pilot studies. However, a key strength of our research lies in its evaluation of the hypothesis that sustainable management practices significantly influence coffee cup quality. Furthermore, this study established a methodological framework for investigating this relationship. Future research expanding the analysis of the chemical composition through untargeted metabolomics, combined with a broader range of management practices, environmental factors, and beverage quality metrics, will contribute to a more comprehensive understanding of the chemical mechanisms underpinning coffee quality and its association with sustainable agricultural practices.