The province of Pastaza is a biodiversity hotspot in the Amazon but lacks up-to-date inventories of its herpetofauna. This study aimed to provide an updated characterization of the richness, composition and conservation status of amphibians and reptiles in different habitats. Between 2013 and 2018, standardized sampling was carried out using quadrats (8 × 8 m) and transects (100 × 20 m), as well as pitfall traps and daytime and night-time visual censuses. A total of 900 h of effort was distributed across six habitats. Coverage estimators, species accumulation curves, range abundance curves, and alpha diversity indices (Shannon, Simpson, and Chao-1) were used for data analysis, as well as similarity indices (Jaccard). A total of 75 species were recorded (51 anurans, eight lizards, 14 snakes and two salamanders), displaying habitat-dependent dominance patterns led by Dendropsophus sarayacuensis and Scinax ruber. Diversity is considered high according to the Chao-1 (19.63–60.53), Shannon–Weaver (2.402–3.223), and Simpson (0.861–0.947) indices, showing interannual variation with a temporary decrease in year 5 and an increase in year 6. The presence of species at risk (VU, n = 26 spp. and EN, n = 2) and high temporal variability highlight the need for continuous monitoring and conservation strategies tailored to specific habitats.