The data consists of total arbuscular mycorrhizal fungi colonisation in fine roots in old growth forests in Central Amazon. Fine roots younger than three months were sampled using the ingrowth core technique in a large-scale nutrient fertilisation experiment. Total mycorrhizal colonisation is given as a mean of the plant community per plot, where five points inside each plot were sampled in the 0-10 cm soil layer. The spreadsheet depicts the percentage of fine root length colonised by different arbuscular mycorrhizal structures (hyphae, arbuscules and vesicles). Samples were collected in February 2018, eight months after the nutrient fertilisation started at the AFEX project area in Manaus, Brazil at the Biological Dynamics of Forest Fragments Project (BDFFP/ INPA). The study was funded by NERC, BDFFP (logistical support) and Brazilian government (student scholarship). Full details about this dataset can be found at https://doi.org/10.5285/52f756a1-a0f6-4991-b21b-4042018a451f