<p>Thermal heat stress is one of the major environmental threats that pose a challenge to agriculture and agrobiodiversity conservation globally. The present study aims to model heat stress in Tharaka-Nithi County and assess its impact on vegetation health across different agro-ecological zones from 2000 to 2023. The study used the vegetation health index, soil moisture index, land surface temperature, aridity index, aspect, area solar radiation, evapotranspiration and albedo as datasets. A GIS ensemble approach, which combined principal component analysis and TOPSIS was used to model thermal heat stress between 2000 and 2023. Multivariate analysis was used for impact assessment on vegetation health between 2000 and 2023. The study revealed an increase in thermal stress. Areas with very high thermal stress increased from a low of 0.11% in 2008 to 14.49% in 2023, while the areas with very low thermal areas decreased from 16.16% in 2000 to 0.15% in 2023. The regression analysis results for various agro-ecological zones across different years showed consistently negative coefficients for heat stress across all zones and years ranging from − 0.38 to − 0.67. This indicates that increased heat stress is associated with a statistically significant decrease in vegetation health, as supported by the low <i>p</i>-values (below 0.05). All zones, except for the tropical alpine, recorded R-squared values above 0.50 in all the years indicating that more than 50% of the variation in vegetation health index can be explained by thermal heat stress. The research concludes that thermal heat stress is a major contributor to the reduced vegetation health in Tharaka-Nithi County from 2000 to 2023, with an increase in thermal heat stress corresponding to a decline in vegetation health. To maintain vegetation health, this comprehensive analysis is crucial for developing adaptive agricultural practices, improving land management and building resilience to climate change.</p>