Although it is clear that soil characteristics and natural plant diversity are intimately related, many of the relationships between heterogeneity of specific soil properties and indicators of plant diversity in different human-dominated ecosystems remain little studied and often contradictory. In this study we investigate the influence of a range of soil properties on alpha, beta and gamma diversity in three land use systems and over two landscape positions in a tropical fragmented landscape in western Ecuador. The land use systems studied were, with increasing human interference, coffee agroforestry systems, pastures and rice. In all land use systems, beta diversity (species turnover) comprised the major part of total species diversity, with the highest relative beta diversity being in coffee agroforestry systems, although this land use type had the lowest total species richness. We showed that soil heterogeneity (expressed as coefficient of variation of properties within plots) is a better predictor of plant diversity than values of soil properties per se. In all land use systems, plant diversity was positively correlated with heterogeneity of various soil properties. With general linear regression models, we showed that for all land use types combined, over 40% of beta and gamma diversity could be explained with the fixed factors land use type and landscape position, in combination with soil heterogeneity (specifically the heterogeneity of magnesium). When looking at individual land use types, up to 80% of beta and gamma diversity in coffee agroforestry could be explained by landscape position and heterogeneity of magnesium. Although for pasture and rice lower percentages of plant diversity could be explained, soil heterogeneity was still a significant predictor. Landscape position was expressed by higher plant diversity in upland soils than in lowland soils, probably as a result of drainage problems in lower lying areas. Our results show that soil and landscape heterogeneity contribute to plant diversity and are therefore important aspects to consider when planning conservation measures. Running heads: Soil heterogeneity and plant diversity.