Despite its significance, net primary productivity is rarely used as an indicator of climate change. The purpose of this study was to assess the spatiotemporal dynamics of vegetation net primary productivity and its response to climate variability in the Welmel watershed, southeastern Ethiopia. The investigation utilized data from the Moderate Resolution Imaging Spectroradiometer, and the Climate Hazards Group Infrared Precipitation with Stations accessed through the Google Earth Engine cloud computing platform. To evaluate the trend and response of net primary productivity to climatic factors, the Mann-Kendall and Theil Sen’s tests, the Pearson correlation coefficient, and stability analysis through the coefficient of variation of net primary productivity were utilized. The analysis of the temporal trend of net primary productivity revealed that the entire watershed, forest, wood, and cultivated land areas exhibited decreasing trends with net primary productivity values of -0.681, -4.361, -1.41, and − 3.25 g C m− 2/year, respectively. On the other hand, shrubs and grazing land displayed increasing trends of 1.15 and 2.04 g C m− 2/year, respectively. The wood and shrubland trends were statistically significant (p < 0.05). In the spatial analysis, an area of 64.6% showed a decreasing trend, whereas 33.78% displayed an increasing trend in net primary productivity values. The areas with stable and unstable variations in net primary productivity accounted for 26.47% and 8.02%, respectively. The net primary productivity of the land cover types and entire watershed were positively correlated with rainfall, however, only forests and woodlands were statistically significantly correlated (p < 0.05). The net primary productivity and land surface temperature were negatively correlated, except for forests and cultivated land, which were positively correlated. The results of this study provide essential information for managing ecosystems, supporting agricultural practices, and enhancing community resilience in a changing climate.