Consumer awareness of the presence of pesticides in fruits and vegetables and associated health risks influences the actions they undertake to reduce their exposure. This study was carried out to explore consumers’ awareness of pesticide residues in fruits and vegetables and perceptions towards associated health effects in Kampala Metropolitan Area (KMA) in Uganda. Eight focus group discussions (FGDs) were done with fruit and vegetables consumers in KMA. The FGDs consisted of females and males living in urban and rural areas. Discussions were recorded and transcribed. The transcripts were coded inductively and analysed using conventional content analysis. Consumers were aware of the presence of pesticide residues in fruits and vegetables. Non-compliance to good agricultural practices, desire to produce good quality fruits and vegetables, and conflict of interest were thought to be the underlying reasons for the contamination. Consumers thought that their health is at risk of chronic and acute health effects, and that this risk is unavoidable. They emphasized that long term exposure to the pesticide residues puts them at risk of conditions like reproductive defects and noncommunicable diseases like cancer, hypertension, obesity, kidney and heart diseases among others. To reduce the risk, consumers were aware of and relied on mitigation measures including washing, peeling, drying and cooking or applied them in combination. Consumers were aware of the presence of pesticide residues on fruits and vegetables, potential short and long term health risks due to exposure, and domestic processing methods to reduce health risks. There is need for authorities to ensure adherence to good agricultural practices and ensure that farmers and consumers understand that pesticide are used to control pests and disease but not to primarily increase shelf life of fruits and vegetables.