The Clouds and the Earth’s Radiant Energy System (CERES) project monitors Earth’s long-term energy balance and produces data products which have improved our understanding of the role clouds and aerosols play in that balance. Cloud property retrievals from the Moderate Resolution Imaging Spectroradiometer (MODIS) and the Visible Infrared Imaging Radiometer Suite (VIIRS) are a major component of many of these data products. It is important for cloud property retrievals to be consistent over the course of the record so that artificial discontinuities are not introduced into the Earth radiation budget record. In practice, the MODIS and VIIRS instruments have different characteristics and different sets of spectral bands so deriving completely consistent cloud properties from the two instruments is a complex task. This paper investigates differences in the cloud properties retrieved from MODIS and VIIRS using the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) instrument as an independent validation source. Particular consideration is given to CALIOP’s sensitivity to optically thin clouds and the effect these clouds have on the retrieved cloud properties, especially cloud thermodynamic phase. Differences in cloud phase and cloud optical depth from MODIS and VIIRS are characterized by different cloud types including multi-layer scenarios. Characterizing these retrieval differences will help understand and mitigate artifacts in the long-term record.