INTRODUCTION: Agriculture is the primary source of income and household food for >75% of rural Kenyans, including people living with HIV (PLHIV), making agricultural yields an important factor in food security and nutrition. Previous studies have shown the interconnectedness of food insecurity, malnutrition, and poor HIV health by elucidating that having one of these conditions increases the likelihood and severity of having another. However, few studies have explored the linkages between agricultural practices, food security and nutrition for PLHIV, or how agricultural livelihood interventions may affect these domains. This study aimed to examine the mechanisms through which an agricultural livelihood intervention can positively or negatively affect agricultural practices, food security, and nutrition for PLHIV. METHODS: From July 2012-August 2013, we interviewed participants with HIV on antiretroviral therapy (ART) enrolled in a pilot randomized controlled trial (RCT) of an agricultural livelihood and finance intervention to understand the mechanisms through which the intervention may have affected HIV health outcomes. The intervention included agricultural and finance training and a microfinance loan to purchase the MoneyMaker hip pump, a human-powered water pump, seeds, and other farming implements. A purposive sample of 45 intervention and a random subset of 9 control participants were interviewed at 12-month endline visit with a subset of 31 intervention participants interviewed longitudinally at both the 3- and 12-month visits. Transcripts were double coded using an inductive-deductive approach and analyzed for impacts of the intervention on agricultural practices, food security, and nutrition using analytic reports for each key theme. RESULTS: All intervention participants described improvements in agricultural practices and yields attributed to the intervention while many also described improvements in income; these changes in turn contributed to improved HIV health, including suppressed viral loads, and a few people noted improved immunologic parameters. Key mechanisms included the knowledge gained from agricultural training which led to improved yields and access to new markets. The use of the irrigation pump was also identified as an additional, lesser important mechanism. All intervention participants reported sustained improvements in food security and nutrition through increased yields and income from the sale of excess crops used to purchase food, and diversification of fresh fruits and vegetables consumed through agricultural production. This led to self-reported weight gain which was a nutritional mechanism towards improved health. CONCLUSIONS: Agricultural and finance interventions that improve farming practices could lead to improved health outcomes through the pathways of improved food security, income, and diversified diet. The results from this study helped the team to enhance the intervention prior to implementation of the larger cluster RCT (cRCT). By understanding how agricultural livelihood interventions act upon pathways towards improved health, policy options can be developed and implemented to include components that are needed to achieve sustainable outcomes. TRIAL REGISTRATION: ClinicalTrials.gov NCT01548599.