Amphibians are threatened globally with at least 43% of species declining and the most important stressor being habitat loss or degradation. Amphibians inhabiting highly biodiverse tropical regions are disproportionately threatened; however, the effects of landscape alterations on amphibian health are virtually unknown. In this study, we utilised non-destructive techniques to compare size (weight, snout-vent length [SVL]), body condition, male secondary sexual features (forelimb width, nuptial pad length) and breeding success (egg number, fertility [percentage fertilised eggs], hatching success) in túngara frogs (Engystomops pustulosus) collected from reference (n = 5), suburban (n = 6) and agricultural (n = 4) sites in Trinidad; characterised by presence/absence of crops/houses. All measured endpoints were negatively impacted in frogs collected from agricultural sites. The largest effect was observed for hatching success (2.77-fold lower) and egg number (2.5-fold lower). Less pronounced effects were observed on male frogs (weight: 1.77-fold lower; SVL: 1.18-fold lower; forelimb width: 1.33-fold lower; nuptial pad length: 1.15-fold lower). Our findings demonstrate negative impacts of agricultural sites on túngara frog health, with the number of viable offspring reduced by almost one third. The methods outlined here are technically simple and low-cost and thereby have potential for application to other species in order to investigate the potential impacts of habitat degradation on amphibian health. Furthermore, as these methods are non-destructive, they could be used to investigate the potential contribution of frog size and/or reproductive capability as a causative factor contributing to population declines in threatened species, which is particularly pressing in tropical regions.