The present study was conducted in Magnesia Prefecture, central Greece, during the period May–June 2007. It aimed at the comparison between conventional and certified organic olive groves with regard to olive and olive oil production, diversity of plants (herbaceous and woody) and diversity and abundance of avifauna. Correlations between variables within herbaceous plants (linear regression) and woody plants (Principal Component Analysis), and the role of integration time of olive groves to the organic system were investigated. Also, finding easily measurable parameters indicating high bird diversity levels within organic and conventional management systems was a main target of the study. According to our findings, neither edible olive yield nor olive oil yield showed significant differences between conventional and certified organic olive groves. There is an increasing trend for alpha and beta diversity of herbaceous plant species, woody plant beta diversity, density and cover of woody plants, and density of breeding birds in certified organic olive groves (10 years) in comparison with conventional ones. The effect of time since the adoption of organic procedures is very important and produces benefits for the biodiversity. In the total olive groves 15 insectivorous, six granivorous and three insectivorous/granivorous birds species were recorded. Nine bird species distinguished by Ward's hierarchical clustering were identified as typical (indicator value, IndVal>50%) of specific farming systems. Among them, the Eurasian jay, associated with the 10-year certified organic olive groves, and the common cuckoo, Orphean warbler and Red-backed shrike, associated with the 6-year certified organic olive groves, should be regarded as characteristic species (IndVal>70%). Conclusively, organic farming favors some aspects of diversity of herbaceous and woody plants of olive grove ecosystems. On the contrary, similar effects on breeding bird diversity and density were not clearly recorded. However, breeding bird density proved a good indicator of their richness.