Biodiversity is declining at unprecedented rates, with species extinctions being an important component of this process. Currently it is almost impossible to evaluate these declines since biodiversity data is lacking even for emblematic species. Recent advances in eDNA marker gene studies promise to deliver the necessary data, but these approaches have almost never been evaluated in the tropics. Here we evaluate whether 1) eDNA metabarcoding may reliably generate frog faunistic data in species-rich tropical areas, 2) the ecological signal in eDNA data is compatible with data from visual and audio encounter survey (VAES), and 3) eDNA data represent a financially viable solution to biodiversity data acquisition. We applied eDNA metabarcoding to investigate frog species occurrence in five ponds in the Chiquitano dry forest region in Bolivia and compared our data with a simultaneous VAES. We find that taxon lists generated with eDNA and VAES correspond closely, and most deviations are attributable to different species’ life histories. The ecological signal in eDNA closely matches the signal from VAES. We find that the cost efficiency of eDNA surveys is mostly influenced by the richness of local fauna and the number of surveyed sites: VAES may be less costly in low-diversity regions, but eDNA quickly becomes more cost-efficient in high-diversity regions, particularly with many sites. The results underline that eDNA is suitable for large-scale biodiversity surveys in high-diversity areas if precautions in data generation and interpretation are taken and this projects spatially extensive standardized biodiversity surveys in the close future.