Polyploidy is a significant component in the evolution of many taxa, particularly plant groups. However, new polyploids face substantial fitness disadvantages due to a lack of same-cytotype mates, and the factors promoting or preventing polyploid establishment in natural populations are often unclear. We develop spatially explicit agent-based simulation models to test the hypothesis that a perennial life history and clonal propagation facilitate the early stages of polyploid establishment and persistence. Our models show that polyploids are more likely to establish when they have longer lifespans than diploids, especially when self-fertilization rates are high. Polyploids that combine sexual and clonal reproduction can establish across a wide range of life histories, but their success is moderated by clonal strategy. By tracking individuals and mating events we reveal that clonal architecture has a substantial impact on the spatial structure of the mixed diploid-polyploid population during polyploid establishment: altering patterns of mating within or between cytotypes via geitonogamous self-fertilization, the mechanisms through which polyploid establishment proceeds, and the final composition of the polyploid population. Overall, our findings provide novel insight into the role of clonal structure in modulating the complex relationship between polyploidy, perenniality, and clonality; and offer testable predictions for future empirical work.