Abstract. The application of UAV-based aerial imagery has advanced exponentially in the past two decades. This can be attributed to UAV operational flexibility, ultra-high spatial resolution, inexpensiveness, and UAV-based sensors enhancement. Nonetheless, the application of multitemporal series of multispectral UAV imagery still suffers significant misregistration errors, and therefore becoming a concern for applications such as precision agriculture. Direct image georeferencing and co-registration is commonly done using ground control points; this is usually costly and time consuming. This research proposes a novel approach for automatic co-registration of multitemporal UAV imagery using intensity-based keypoints. The Speeded Up Robust Features (SURF), Binary Robust Invariant Scalable Keypoints (BRISK), Maximally Stable Extremal Regions (MSER) and KAZE algorithms, were tested and parameters optimized. Image matching performance of these algorithms informed the decision to pursue further experiments with only SURF and KAZE. Optimally parametrized SURF and KAZE algorithms obtained co-registration accuracies of 0.1 and 0.3 pixels for intra-epoch and inter-epoch images respectively. To obtain better intra-epoch co-registration accuracy, collective band processing is advised whereas one-to-one matching strategy is recommended for inter-epoch co-registration. The results were tested using a maize crop monitoring case and the; comparison of spectral response of vegetation between the UAV sensors, Parrot Sequoia and Micro MCA was performed. Due to the missing incidence sensor, spectral and radiometric calibration of Micro MCA imagery is observed to be key in achieving optimal response. Also, the cameras have different specifications and thus differ in the quality of their respective photogrammetric outputs.