Fruit tree cultivation holds significant potential for enhancing household food security and dietary diversity among smallholder farmers, particularly during periods of crop failure or non-cropping seasons. This study assessed the diversity of fruit trees on farms and their relationship with food security across four agro-ecological zones (AEZs) in Western Kenya. Using a stratified random sampling design, 296 households were surveyed, categorized into three groups: those exposed to a fruit cultivation programme (‘FRUIT’), a hygiene programme (‘WASH’), and a non-intervention control group (‘CONTROL’). Data were collected on socio-economic status, farm characteristics, and fruit tree diversity. A total of 32 fruit tree species comprising 8,376 individuals were identified, with only 9 species and 180 individuals being indigenous. Exotic species such as Mangifera indica, Persea americana, and Psidium guajava were most common, found on 80%, 77%, and 62% of farms, respectively. Median species richness was 4.0 and median tree abundance 13 per farm. Diversity measures differed significantly across AEZs (p < 0.001), and ‘CONTROL’ households had significantly fewer indigenous trees (p = 0.039). Male-headed households owned more exotic trees than female-headed ones (p = 0.030). Food insecurity was widespread, with 90% of households reporting scarcity, peaking in April and May. The average household hunger scale was 5.1 and average number of food-insecure months was 3.6. Multivariate analysis indicated that hunger scale was driven by poverty, ethnicity, and farm size rather than fruit tree diversity. The findings highlight the need for targeted interventions promoting indigenous fruit tree cultivation, especially timed to address seasonal food shortages among vulnerable populations.