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Normalized difference vegetation index (NDVI) and normalized difference red-edge index (NDRE) are vegetation indices commonly used in agriculture to provide information on crop’s growth and health. Here, we investigated the sensitivity of both indices to management practices in lowbush blueberry fields. Images of the experimental plots were collected with a multispectral camera installed on an unmanned aerial vehicle. Both NDVI and NDRE values were significantly higher in fertilized plots than in controls (0.88 ± 0.03 vs. 0.79 ± 0.03 for NDVI, and 0.37 ± 0.01 vs. 0.33 ± 0.01 for NDRE) due to fertilization effect on vegetative growth. The increase was higher under mineral than organic fertilization during the two first phases of the cropping system (by ∼0.3 and ∼0.2 for NDVI and NDRE, respectively). NDRE was not affected by thermal pruning and fungicide application but was negatively correlated with Septoria infection level. NDVI was more strongly correlated with stem length than NDRE, but unlike NDRE, NDVI was not impacted by the development of reproductive shoots during the harvest phases. Overall, the results indicate that although both index values are correlated, their sensitivity to changes in canopy characteristics differs depending on the cropping phase. Further research must be conducted to relate these indices to blueberry’s nutrient status.