Phytophthora wilt, caused by Phytophthora capsici Leon., is the most devastating disease of chilli in Bhutan. In this study, effects of bed heights to improve soil drainage, animal manures and fungicides on Phytophthora wilt on chilli were evaluated on naturally infested plots at the wet lowlands site of Bhur and in a farmer’s field at a drier, higher altitude site at Darachu in Bhutan. The experimental design was a split-plot arrangement of a randomised complete block. Bed height (flat or raised) was the main plot with amendments (poultry manure, cattle manure) or fungicide drenches (metalaxyl or potassium phosphonate) as subplot treatments. Aged manures (28,000 kg DW/ha) were applied to the field one week before planting. Chilli seedlings in the nursery bed were drenched with 1 g a.i./L potassium phosphonate or 10 mg a.i./L metalaxyl 24 hours prior to transplanting. Plant survival was significantly higher on raised beds than flat beds at Bhur ( p  = 0.0105), but not Darachu, although marketable yields were significantly higher on raised beds at both sites. At Darachu, poultry manure significantly improved plant survival (50%), as did cattle manure (41%) compared to unamended control plots (25%). Similar results were found at Bhur, with survival on poultry manure amended soils (40%) and cattle manure (34%), both significantly higher than on unamended soils (20%). Both fungicides significantly improved plant survival ( p  < 0.0001) and marketable yield ( p  < 0.0001) at both sites. Yields at the high-altitude, drier site at Darachu were generally higher than at the wet lowlands site at Bhur. Marketable yields on phosphonate-treated plots at both Bhur and Darachu, (16.8 and 19.1 tonnes/ha, respectively) and metalaxyl-treated plots (15.4 and 17.5 tonnes/ha) were significantly higher than on untreated plots (6.0 and 7.5 tonnes/ha). A highly significant ( p  = 0.0007) benefit of combining raised beds planting with manure and fungicide treatments on yield was observed at the wet lowlands site, but not at the drier site. Integrating raised bed planting with the application of poultry manure and fungicides is likely to significantly reduce yield losses of chilli due to Phytophthora wilt in different regions of Bhutan.