Trends in crop phenometrics reveal the influence of climate variability and change on crop growth and development. However, the trends are less clear in fragmented tropical smallholder landscapes, because there is high spatial and temporal variability in crop phenology. Frequent historical and high spatial resolution (≤30 m) Earth observations are needed to track changes in crop phenology in fragmented landscapes but are often unavailable. The spatial–temporal gap can be closed by integrating infrequent high spatial resolution Earth observations with low spatial/high temporal resolution observations through data fusion. We fused 30 m resolution Landsat and 250 m resolution MODIS imagery to investigate trends in crop phenology from 2000 to 2020 in a fragmented agricultural landscape of Ethiopia. We used the Enhanced Spatial and Temporal Adaptive Reflectance Fusion Model (ESTARFM) that had recently been modified for application in fragmented agricultural landscapes. We used the non-parametric Mann–Kendall test for crop phenology trend analysis. Crop phenology based on Landsat–MODIS fusion was compared to MODIS-based crop phenology without fusion. We found data fusion yielded a smaller magnitude of changes in the start of season (SOS: -0.2-day-y−1) and end of season (EOS: -0.50-day-y−1) compared to MODIS SOS (-0.5-day-y−1) and EOS (1.38-day-y−1) due to MODIS-related mixing with the surrounding natural vegetation in the fragmented agricultural landscape. EOS showed a faster rate of change compared to SOS over the 21-years. The Landsat and MODIS fusion captured spatial variation in the timing and magnitude of change specific to crops and their growing environment, which has implications for adaptation strategies. Our results highlight the importance of long-term data fusion to improve the spatial dimension of crop phenology time series analysis. Integrating time series land cover maps into the data fusion processing chain could further improve long-term data fusion for crop phenology trend analysis.