Ecological restoration is considered a tool for repairing anthropogenic habitat disturbances, but the biodiversity recovering needs to be monitored. Here we evaluate a comprehensive approach for biodiversity: Biodiversity Quality, which comprises a set of 10 indices representing different components of diversity and providing an holistic overview. This approach was tested in a hyper-diverse insect group, the Ichneumonidae family in three different levels of conservation, i.e., a degraded area, a well-conserved area and an area undergoing ecological restoration for 10–15 years. Comparisons were done in three different ecosystems from southern Ecuador, i.e., Andean forest, rainforest and dry forest. We also compared the species assemblages through beta diversity indices. A total of 36 Townes style white Malaise traps were installed at three different conservation levels in 12 natural reserves, and all Ichneumonid insects collected were sorted, mounted and identified to operational taxonomic units (OTUs). A total of 2929 individuals in 708 OTUs were collected, which represented 1264.78 g of biomass. No differences were found between conservation levels, but all indices showed significant differences when comparing ecosystem types. Andean forests had significantly more richness, diversity, population and biomass than the other ecosystems, and less dominance and rarity than dry forests. Species composition of Ichneumonidae assemblages were also different between ecosystems and not so between conservation levels. When comparing in every ecosystem separately, degraded areas in dry forest had significantly more density and biomass than conserved areas. This represents a first attempt of applying this comprehensive approach in such a species-rich family.