Native and exotic species richness is expected to be negatively related at small spatial scales where individuals interact, and positive at larger spatial scales as a greater variety of habitats are sampled. However, a range of native-exotic richness relationships (NERRs) have been reported, including positive at small scales and negative at larger scales. We present a hierarchical metacommunity framework to explain how contrasting NERRs may emerge across scales and study systems, and then apply this framework to NERRs in an invaded winter annual plant system in south-west Western Australia. We analysed NERRs at increasing spatial scales from neighbourhoods (0.09 m2) to communities (225 m2) to metacommunities (>10 ha) within a multi-level structural equation model. In contrast to many previous studies, native and exotic richness were positively related at the neighbourhood scale and were not significantly associated at larger scales. Heterogeneity in soil surface properties was weakly, but positively, associated with native and exotic richness at the community-scale. Metacommunity exotic richness increased strongly with regional temperature and moisture availability, but relationships for native richness were negative and much weaker. Thus, we show that neutral NERRs can emerge at larger scales due to differential climatic filtering of native and exotic species pools.