This bat lives in caves in dry forests associated with calcareous outcrops and appears to require caves to roost. In a study, population sizes changed throughout the year; the population of Dois Irmãos cave was larger in September and October, probably due to the recruitment of young, and in March and April, due to the return of pregnant females. In all populations the number of females exceeded that of males and the number of adults was greater than that of young. The species is closely associated with karstic environments (Aguiar et al. 2010).

Young individuals were captured from July to November and adults were captured throughout the year. Lonchophylla dekeyseri occurred in relatively small populations and demonstrated fidelity to the shelter, remaining for at least one year in the same cave (Aguiar et al. 2006). The reproductive pattern presented by the species was seasonal monoestry, with young being born in the dry season, probably due to the greater food availability at this time of the year. A nursery system seems to occur, as the females were never observed carrying their young (Aguiar et al. 2006). Females were found to occur in greater numbers than males, suggesting harem formation. Emergence from the shelter occurred in the first hours after dusk; returning just before dawn during the rainy season and returning around midnight and just before dawn during the dry season. The activity pattern observed was unimodal, changing to bimodal in the dry season. Activity period could be related to the blossoming and nectar production patterns of the flowers visited by L. dekeyseri.

It is a nectarivorous bat, but can use other resources such as fruits and insects. Lonchophylla dekeyseri feeds upon pollen in the dry season, when this resource is more plentiful, and consumes more insects and fruits in its diet during the rainy season, when nectar is scarce and insects are abundant. Bat hair analysis showed 7 types of pollen, mainly from Pseudobombax sp., Bauhinia sp. and Lafoensia sp. This species pollinates typical plants of the Cerrado. Bat-pollinated plants flowered during the dry season with sequencial peaks, probably a mechanism which may avoid competition for pollinators by other plants maximizing pollinator efficiency. The occurrence of more than one type of pollen in the same bat hair sample was common, indicating visits to several plant species during only one night (Coelho 1998).

Lonchophylla dekeyseri is the only endemic bat species of the Cerrado habitat in Brazil. Its type locality is given as eight kilometres north of Brasilia, Federal District (Coelho 1998, Eisenberg and Redford 1999), and the species is known from Brazil and eastern Bolivia (Griffiths and Gardner 2008). While the species appears to be fairly widespread, the distribution appears to be patchy within its geographic range.