Agroecological studies on sugarcane intercropping commonly generate complex datasets. A generic database (AEGIS – Agro-Ecological Global Information System) has been developed to facilitate the use of these datasets. The data described in this paper includes data from 8 experiments carried out on Reunion Island from 2012 to 2021 under three soil and climatic conditions to assess the capacity of cover crops in the sugarcane inter-row to control weed growth. Each experiment consisted of the comparison of three treatments in the inter-row: i) sugarcane with chemical weeding, ii) sugarcane with a cover crop sowed in the inter-row, and iii) sugarcane with spontaneous weed flora in the inter-row. The datasets contain data for sugarcane and cover crop observations (e.g., yield), weed flora, including 104 weed species (e.g., ground cover), crop management (including manual and chemical weedings), soil analyses, and daily weather. This dataset provides an adequate experimental dataset to calibrate or validate crop model simulations under intercropping.