Organic amendments can improve soil quality which has knock-on environmental and agronomic benefits. However, the use of new and emerging organic amendments such as biochar and brown coal waste (BCW) in soil systems requires continuous holistic assessments for robust consensus building in their environmental and agricultural applications. To examine the application of BCW and woodchip biochar (BIO) in agroecosystems, secondary data from literature on environmental (soil, air and water) aspects were compiled with primary agronomic data from a 3-year multicropping field trial and collated with supplementary data on economic factors (e.g. cost and availability). For the field trial, replicated plots were amended with FYM (for comparative reasons), BCW and BIO at 30, 24.2 and 12.8 for t ha–1, respectively, with and without NPK and cultivated in a cropping sequence of maize, potato and barley. At the end of each season, soils were characterised for pH, cation exchange capacity (CEC) and fertility (macronutrient contents) in addition to nutrient uptake, nutritional quality and yield of crops. Compared with FYM, biochar and BCW were found to be associated with greater improvements in soil quality (e.g. building of soil structure and C sequestration) and knock-on water and air quality benefits mainly facilitated via increased cation retention and humic-linked sorption which abated gaseous emission and mitigated nutrient and heavy metal leaching. These along with variable improvements in soil chemistry, fertility and nutrient uptake in the agronomic field trial accounted for increased mean crop yield across treatments (higher with NPK): FYM (32.7 and 71.7%), BCW (33.5 and 60.1%) and BIO (21.8 and 48.2%). Additionally, biochar and BCW have lower pollutant (e.g. heavy metals) contents and were found to provide additional sustainability and net abatement cost-benefits. While the agronomic benefits of biochar and BCW were slightly lower compared with that of FYM, their lower environmental footprints and associated sustainability benefits are clear advantages for their adoption in environmental and agricultural applications.