Nascent polypeptide cofactors NAC and SRP select for gene targets, regulating their expression in a tissue and/or cell specific manner to regulate heart morphogenesis. Our work suggests that the posterior determining Hox gene Abd-B is a target of Nacα, as the knockdown of Nacα led to Abd-B misexpression and disruption of heart morphogenesis through failure of cardiac remodeling during metamorphosis. Knockdown of SRP subunits each led to distinct heart defects: SRP72 knockdown disrupted conical chamber morphogenesis, SRP-Rβ targeted internal valve cells, SRP54 led to missing cardiomyocytes, SRP19 led to loss of anterior segment of the heart, while SRP68 led to a no heart phenotype similar to Nacα knockdown. Future work can help uncover the nature of the distinct phenotypes whether due to dissimilar KD levels or targeting of unique transcripts by individual SRP subunits to direct different cell fates.