MicroRNA (miRNA) regulation clearly impacts animal development, but the extent to which development—with its resulting diversity of cellular contexts—impacts miRNA regulation is unclear. Here, we compared cohorts of genes repressed by the same miRNAs in different cell lines and tissues and found that target repertoires were largely unaffected, with secondary effects explaining most of the differential responses detected. Outliers resulting from differential direct targeting were often attributable to alternative 3′ UTR isoform usage that modulated the presence of miRNA sites. More inclusive examination of alternative 3′ UTR isoforms revealed that they influence ∼10% of predicted targets when comparing any two cell types. Indeed, considering alternative 3′ UTR isoform usage improved prediction of targeting efficacy significantly beyond the improvements observed when considering constitutive isoform usage. Thus, although miRNA targeting is remarkably consistent in different cell types, considering the 3′ UTR landscape helps predict targeting efficacy and explain differential regulation that is observed. Display omitted •Cellular context does not detectably affect the majority of miRNA targets•Differential 3′ UTR isoforms explain cell-type-specific targeting that is observed•Considering the 3′ UTR landscape improves prediction of targeting efficacy•miRNA-mediated repression shapes the 3′ UTR landscape MicroRNAs function in many biological contexts, but the extent to which these different contexts modulate the cohort of genes regulated by a miRNA was unclear. Nam et al. show that miRNA targeting is remarkably consistent between different cell types and that most differential targeting that is observed is explained by differences in 3′ UTR isoforms.