Abstract 1. This study examines limitation of nesting resources for leaf‐litter and twig‐nesting ants as a mechanism of diversity loss across an intensification gradient of coffee production in Colombia. Twelve farms were selected and classified into four management types: forest, polygeneric shade coffee, monogeneric shade coffee, and sun coffee (unshaded coffee monocultures). 2. At each of the farms, four treatment subplots were established at the corners of each of 10 25 m 2 plots: (i) twig augmentation (adding 10 empty bamboo twigs); (ii) litter augmentation (tripling existing litter profile); (iii) twig and litter augmentation; and (iv) no manipulation control, for a total of 480 subplots. A twig addition experiment was also performed on coffee bushes. 3. The results showed significantly more ant colonies in the forest and monogeneric shade coffee litter augmentation plots after 4 months. Litter‐nesting ant species richness was higher in all three shade systems than in the sun coffee. The identities of ants nesting on coffee bushes were different from those in the soil level litter. Fewer species nested in bamboo twigs placed in litter in the most intensive systems. 4. More ants nested in the resource addition treatments, and more ant species were found in forested habitats; however, a single mechanism cannot explain the observed patterns. It was concluded that a combination of bottom‐up and top‐down effects might lead to the loss of associated fauna with the intensification of these agroecosystems.