The aim of this study is to determine maize and paddy yield difference under organic and conventional farming in Bhutan, and subsequently determine factors influencing this difference. Results from arithmetic mean comparison show that maize organic yield is on average 40.9% lower compared to conventional, and 36.9% lower for paddy. Simple linear regression is used to determine factors influencing the yield. Findings indicate that, in contrast to other studies, female-headed households are much more productive than male-headed households. Temperature plays a significant role in determining yield of both crops, so does the use of machinery. Surprisingly, education, labor, and precipitation showed no significant impact on the level of output. Alongside gender, proximity to markets and use of agrochemicals had a major influence on the yield of both crops. Analysis also showed that elevation and climate characteristics heavily influence the yield, this is depicted by yield comparisons across different agro-ecological zones.