Coffee breeding based on root traits is important to identify productive genotypes under adverse environmental conditions. This study assessed the diversity of root traits in Coffea canephora and its correlation with plant height and crop yield. Undisturbed soil samples were collected down to 60 cm from 43 coffee genotypes, in which one of them was propagated by seed and all others by stem cutting. The roots were washed, scanned, and processed to quantify root length density, root volume, root superficial area, and root diameter. Additionally, plant height and crop yield were also assessed. Root length density ranged from 40 to 1411 mm cm−3, root volume from 6 to 443 mm3 cm−3, root superficial area from 61 to 1880 mm2 cm−3, and root diameter from 0.6 to 1.1 mm. Roots were concentrated in the topsoil (0–20 cm) for most genotypes. In deeper depths (30–60 cm), root length density, root volume, and root superficial area were higher in genotypes 14, 25, 31, and 32. Positive correlations were found between root traits and both plant height and crop yield. The results of this work may contribute to the overall cultivation of C. canephora, specially for crop breeding in adverse environmental conditions.