Guava (Psidium guajava) is a highly nutritious fruit tree thriving across diverse agro-climatic zones in Eastern Africa. Despite its potential, guava utilization in Kenya remains limited, largely due to inadequate agronomic knowledge, weak farmer integration in value chains, and limited awareness of the crop’s nutritional and economic value. Additionally, the morphological diversity within Kenyan guava germplasm remains poorly documented. This study aimed to assess the morphological variation among guava accessions across four contrasting agroecological regions: Western, Rift Valley, Eastern, and the Coastal region. Field assessments were conducted on 105 guava trees, and 20 fruits per tree were sampled for analysis of morphological traits. Significant regional differences were observed. Trees from the Rift Valley exhibited the largest mean diameter at breast height (DBH) at 51.0 cm, while Coastal trees had the smallest (26.1 cm; p = 0.003). Coastal fruits had a slightly thicker pericarp (5.17 mm) compared to Eastern region fruits (3.96 mm), whereas Eastern fruits exhibited significantly greater pulp weight (19.0 g vs. 10.9 g; p = 0.001). Seed weight proportion was highest in fruits from Coastal and Western regions. Fruit shapes varied, with round (43%), obovate (25%), and ovate (14%) forms being most common. Most fruits (93%) had yellow, orange, or reddish pulp; only 7% had white pulp. Cluster analysis based on standardized morphological traits revealed two major groups, differentiating accessions primarily by fruit size, pulp weight, and seed content. These findings provide a foundation for targeted guava selection and breeding in Kenya, supporting both fresh consumption and processing-oriented value chains.