Traditional home gardens in southern Ethiopia are acknowledged for equitable gender involvement in agriculture. However, these age old traditional home gardens are changing towards commercialization of khat. Smallholders commercialization to khat may affect the gender participation in agricultural activities. Thus, the effect of change in home gardens commercialization to khat on gender participation in agricultural activities and its variation between different resource endowed farmers were studied based on a survey of 120 farm households and focus group discussions. The study revealed that men played major role in land preparation, planting and management of all crops grown within home gardens. The involvement of men in all khat related activities were higher than all crops whereas women’s involvement in khat was the least of all crops. Women were involved more on management and harvesting of vegetables and root crop and harvesting of enset. Land preparation of coffee, cereal crops and root crops involved more of both men and women as compared to other crops. The involvement of both men and women in the harvesting of coffee and annual cereals were higher than other crops while harvesting of khat and fruit trees were dominated by men. Resource endowment caused variation in gender participation in agriculture as women in large farm households involved more on the harvesting of enset while those in medium and small farm household more on land preparation for enset and annual cereals. Understanding the effect of commercialization to khat on gender participation helps to design tailored sustainable development options to enhance gender participation in agriculture.