Phka Rumdoul is a premium aromatic rice variety highly valued in Cambodia for its fragrance, primarily attributed to 2-Acetyl-1-pyrroline (2-AP). The intensity of this aroma varies across regions, suggesting strong environmental and agronomic influences. This study investigated the impact of different agro-systems on 2-AP accumulation in Phka Rumdoul by examining the relationship between soil’s physicochemical properties and grain 2-AP content. Samples were collected from 33 fields across nine provinces, representing five cultivation practices: conventional tillage (CT), conservation agriculture (CA), sustainable rice platform (SRP), organic rice farming (ORF), and green manure (GM). The soil samples were analyzed for pH, soil moisture, total carbon, organic matter, total nitrogen, total phosphorus, cation exchange capacity, exchangeable Ca, Mg, K, and Na, and C/N ratio. Rice grains were analyzed for 2-AP concentration (µg/g) using gas chromatography mass spectrometry (GC-MS) based on the internal standard and ion fragments. Principal component analysis (PCA) was employed to see the correlation of soil properties contributing across different agro-systems and 2-AP levels. The results showed that CA and SRP practices produced significantly higher 2-AP levels compared to CT. In Kampong Thom, CA improved soil properties such as organic carbon and exchangeable nutrients, which correlated with increased 2-AP content. However, variation in 2-AP levels under the same practice (e.g., ORF) across provinces suggests that environmental factors and possible genetic differences within the variety also play roles. In conclusion, CA improves both soil quality and aroma accumulation in Phka Rumdoul rice. Future studies using genetically uniform seeds and standardized post-harvest handling are recommended to better understand the effects of agroecological factors on rice aroma.