In intensively cultivated landscapes, many archaeological remains are buried under the ploughed soil, and detection depends on crop proxies that express subsurface features. Traditionally these proxies have been documented in visible light as contrasting areas of crop development commonly known as cropmarks. However, it is recognised that reliance on the visible electromagnetic spectrum has inherent limitations on what can be documented, and multispectral and thermal sensors offer the potential to greatly improve our ability to detect buried archaeological features in agricultural fields. The need for this is pressing, as ongoing agricultural practices place many subsurface archaeological features increasingly under threat of destruction. The effective deployment of multispectral and thermal sensors, however, requires a better understanding of when they may be most effective in documenting archaeologically induced responses. This paper presents the first known use of the FLIR Vue Pro-R thermal imager and Red Edge-M for exploring crop response to archaeological features from two UAV surveys flown in May and June 2019 over a known archaeological site. These surveys provided multispectral imagery, which was used to create vegetation index (VI) maps, and thermal maps to assess their effectiveness in detecting crop responses in the temperate Scottish climate. These were visually and statistically analysed using a Mann Whitney test to compare temperature and reflectance values. While the study was compromised by unusually damp conditions which reduced the potential for cropmarking, the VIs (e.g., Normalised Difference Vegetation Index, NDVI) did show potential to detect general crop stress across the study site when they were statistically analysed. This demonstrates the need for further research using multitemporal data collection across case study sites to better understand the interactions of crop responses and sensors, and so define appropriate conditions for large-area data collection. Such a case study-led multitemporal survey approach is an ideal application for UAV-based documentation, especially when “perfect” conditions cannot be guaranteed.