The benthic cover data described here result from benthic photo-quadrat surveys conducted by the NOAA Coral Reef Ecosystem Program (CREP) in hard bottom shallow water (< 15 m) habitats in Timor-Leste during reef fish surveys surveys at 150 sites that were selected using a stratified random sampling design in June 2013, and along transects at fixed climate survey sites in September-October 2014 (10 sites and 8 sites, respectively). Climate sites were established by CREP to establish ecological baselines for climate change by measuring multiple features of the coral reef environment (in addition to the data described herein) over time. The reef fish surveys were conducted to generate baseline data on the nearshore coral reef fish assemblages and associated benthic communities around Timor-Leste's north coast and Atauro Island. Percent benthic cover for each site is estimated from a photo-transect (30 photographs, taken at 1-m intervals, 10+ points analyzed per photograph using Coral Point Count with Extensions). NA values represent situations where images were either not gathered or not analyzed. These benthic cover data for Timor-Leste provide an estimate of the benthic community composition at each survey site, and give context to the results from the other survey components. The benthic images, and the associated reef fish survey data and parameters measured to establish ecological baselines for climate change are documented separately.