This article describes the technical specifications and configuration of a multirotor unmanned aerial vehicle (UAV) to acquire remote images using a six-band multispectral sensor. Several flight missions were programmed as follows: three flight altitudes (60, 80 and 100 m), two flight modes (stop and cruising modes) and two ground control point (GCP) settings were considered to analyze the influence of these parameters on the spatial resolution and spectral discrimination of multispectral orthomosaicked images obtained using Pix4Dmapper. Moreover, it is also necessary to consider the area to be covered or the flight duration according to any flight mission programmed. The effect of the combination of all these parameters on the spatial resolution and spectral discrimination of the orthomosaicks is presented. Spectral discrimination has been evaluated for a specific agronomical purpose: to use the UAV remote images for the detection of bare soil and vegetation (crop and weeds) for in-season site-specific weed management. These results show that a balance between spatial resolution and spectral discrimination is needed to optimize the mission planning and image processing to achieve every agronomic objective. In this way, users do not have to sacrifice flying at low altitudes to cover the whole area of interest completely.