Premise of the study Shifts in ploidy level will affect the evolutionary dynamics of genomes in a myriad of ways. Population genetic theory predicts that transposable element (TE) proliferation may follow because the genome wide efficacy of selection should be reduced and the increase in gene copies may mask the deleterious effects of TE insertions. However, to date the evidence of TE proliferation following an increase in ploidy is mixed, with some studies reporting results consistent with this scenario and others signs of genome downsizing. Methods We used high-coverage whole genome sequence data to evaluate the abundance, genomic distribution, and population frequencies of TEs in the self-fertilizing recent allotetraploid Capsella bursa-pastoris, a species with prior evidence for genome-wide reductions in selection at the amino acid level since the transition to selfing. We then compared the C. bursa-pastoris TE profile with that of its two parental species, outcrossing C. grandiflora and self-fertilzing C. orientalis. Key results We found no evidence that C. bursa-pastoris has experienced a large proliferation of TEs. Instead, the abundance, both overall and near genes, as well as the population frequencies of TEs, are intermediate to that of its two parental species C. grandiflora and C. orientalis. Conclusions The lack of shift in TE profile beyond additivity expectations in C. bursa-pastoris can be because of variety of factors. In general, we argue that allopolyploid lineages that retain high outcrossing should provide a “perfect storm” for TE proliferation, while highly selfing polyploids may generally experience TE loss.