The importance of forests for biodiversity conservation has been well recognized by the global community; as a result, conservation efforts have increased over the past two decades. In Ecuador, the lack of integrated information for defining and assessing the status of local ecosystems is a major challenge for designing conservation and restoration plans. Thus, the objectives of this study were (1) to examine the regeneration status of cloud forest remnants, some of which had experienced past human disturbance events, (2) to explore a local rural community’s traditional ecological knowledge (TEK) relevant for restoration and (3) to investigate the integration between TEK and ecological science-based approaches. A survey of regeneration status was conducted in four remnants of cloud forests (n = 16) in Cosanga, Napo Province, in the Andes of northeastern Ecuador. The species of young trees (0.5–5 m height) were identified over 0.16 ha. In-depth interviews of individuals from local communities (n = 48) were conducted to identify socio-ecologically important native species. The results showed significant differences (p < 0.001) in species richness and the stem density of seedlings and saplings in gaps. The stem density of Chusquea sp., a bamboo species, explained 63% of the variation in species richness and 48% of the variation in the abundance of seedlings and saplings between plots. Informants cited 32 socio-ecologically important species, of which 26 species were cited as sources of food and habitats for wildlife. The ranking of species based on a relative importance index and a cultural value index—taking into account both the spread of knowledge among local informants and the multiplicity of uses—revealed that Hyeromina duquei, Citharexylum montanum, Eugenia crassimarginata and Sapium contortum were traditionally the most valuable species for both humans and wildlife. Informants also recommended 27 species for future planting, of which 19 species were amongst the rarest species in the regeneration survey. In conclusion, the results demonstrate a synergy between TEK and ecological science-based approaches (regeneration survey) to natural ecosystem research. Thus, traditional ecological knowledge can provide insights into ecosystem–plant–animal interaction, and to identify native species useful for both humans and wildlife for forest restoration projects to reconnect isolated cloud forest fragments.