Trachymyrmex intermedius inhabits wet and moist forest habitats. It seems to prefer relatively open areas with a thin litter layer. Nests are in the soil, with a spherical chamber just beneath the surface. The chamber is approximately 5cm diameter, containing a spongy white fungus garden.
At La Selva Biological Station it is relatively common in the laboratory clearing. Various attine researchers, including Jim Wetterer and Ted Schultz, have excavated colonies in the clearing. Azur Moulaert found workers cutting leaves of Callophyllum brasiliense in the open second growth of the La Guaria Annex of La Selva. I have collected ground foragers on the grounds of an ecotourism lodge in Tortuguero and in scrubby second growth forest at 800m on the Pacific slope below Monteverde.
Like Trachymyrmex in general, the species is extremely rare in Winkler samples of sifted litter, suggesting that it avoids areas of deep leaf litter or is poorly sampled by Winkler sifting for some other reason.