To assess the availability and marketing of ultra-processed foods (UPFs) in modern retail food outlets (supermarkets and minimarts) in Kenya and associated factors. This cross-sectional study was conducted in Kenya from August 2021 to October 2021. Variables included; the geographic location and the socioeconomic status levels (SES), the food items displayed for sale and advertised in the stores, and locations in the stores such as the entrance. Three counties in Kenya (Nairobi - urban, Mombasa - coastal tourist, and Baringo- rural). Each county was stratified into high and low SES using national poverty indices. Food outlets that offered a self-service, had at least one check-out, and had a minimum of two stocked aisles were assessed. Of 115 outlets assessed, UPFs occupied 33% of the cumulative shelf space. UPFs were the most advertised foods (60%) and constituted 40% of foods available for sale. The most commonly used promotional characters were cartoon characters (18%). UPFs were significantly more available for sale in Mombasa (urban) compared to Baringo (rural) (Adjusted prevalence rate ratios (APRR): 1.13, 95% confidence interval (CI): 1.00-1.26, p=0.005). UPFs advertisements were significantly higher in Mombasa ((APRR): 2.18: 1.26-3.79, p= 0.005) compared to Baringo and Nairobi counties. There was a significantly higher rate of advertisement of UPFs in larger outlets ((APRR): 1.68: 1.06-2.67 p=0.001) compared to smaller outlets. The high marketing and availability of UPFs in modern retail outlets in Kenya calls for policies regulating unhealthy food advertisements in different settings in the country.