This study aimed to establish a strategy for drought-tolerant selection in Arabica coffee genotypes in Brazil, combining field trials under natural conditions with controlled growth condition experiments. A group of genotypes was evaluated in the greenhouse using 28 morphological, anatomical, and physiological traits. In addition, the productivity of genotypes was evaluated in the field. Under water deficit in the greenhouse, 13 studied traits showed significant genetic variance. For these traits, the heritability coefficients estimated based on the progeny mean ranged from 65 to 92%. A selection index combined with predicted means was applied at these traits to select four progenies for drought tolerance under greenhouse conditions. Under field conditions, the selection applied to genetic values that favored positive genetic gains in four progenies, indicating the potential use of these cultivars for breeding advanced generations. The selection results of coffee plants under greenhouse conditions matched the selection results in the field in a water-deficit region by 50% based on productivity; thus, two genotypes (H419-3-3-7-16-11 and H516-2-1-1-7-2) were identified that have both the productivity and morpho-anatomical traits that confer greater drought tolerance. Finally, we discussed possible strategies for the development of drought-tolerant cultivars.