Abstract Background Home gardens (HGs) provide perspectives for conservation of plant genetic resources while contributing to improving livelihoods. However, knowledge of local factors shaping their ownership, plant diversity (PD) and structure is still limited especially in West-Africa, where food insecurity is acute. This is critical to ensure effective mainstreaming of HGs into future biodiversity conservation and food production policies. Methods Socio-economic and PD data were obtained from individual interviews ( n  = 470) and gardens inventories ( n  = 235) spanning humid, sub-humid and semi-arid zones of Benin. Generalised Linear Models, Hierarchical Cluster Analysis, Principal Component Analysis and Simple Correspondence Analysis were performed to examine socio-economic characteristics (age, gender, education level and main economic activity) affecting HGs ownership, and their effect coupled with intrinsic HGs characteristics (size, age) on PD and structure within HGs, across contrasting bio-geographical regions. Results HG ownership was significantly dependent upon a complex relationship between age, gender and education level of the farmers. The probability to own HG increased with age with an early involvement in home gardening for women. Similarly, with increasing age, it was more likely to find a male owner than a female owner among the uneducated informants and those of primary school. Inversely, it was more likely to find female owner than a male owner among secondary school level or more. PD increased with increasing owner age and size of the HG. Larger and more diversified HGs were found in sub-humid and semi-arid zones while smaller and less diversified HGs were encountered in the humid zone. HGs were multi-layered. Based on the prevailing plant groups, three categories of HG were distinguished: Herb based gardens, Herb and Shrub/Trees based gardens, and Palm and Liana based gardens. Their prevalence was dependent upon bio-geographical zones and HG owner socio-economic characteristics, with herbs based HGs being mainly associated to women. Conclusion Results suggest effects of complex interactions between socio-economic factors on HG ownership, and influence of these effects combined with intrinsic characteristics of HGs on PD. The early involvement of women in home gardening and their particular interest in herbs and shrubs are important assets for future conservation strategies based on HG and food production. Interventions are required to interfere with declining PD in HG across generations to .