Non-LTR retrotransposon proteins copy their RNA template into a genome via coordinated nicking and reverse transcriptase activities of target-primed reverse transcription. Mechanisms by which the first-strand cDNA becomes stably inserted duplex, including requirements for junction formation at the cDNA 3' end and second-strand synthesis, are unknown. We screened for cellular factors that influence site-specific transgene synthesis into the human genome by an R2 retrotransposon protein. We discover that insertion lengths and junction signatures differ based on alternative repair processes involving ATR-dependent Polymerase θ end-joining, 53BP1-directed Shieldin/CST-Polα-primase fill-in synthesis, or limited strand annealing dependent on CtIP-MRN. These insights shed light on how genome-primed cDNA synthesis by a non-LTR retrotransposon protein can support stable new gene insertion, with major implications for native retrotransposon mobility and genome engineering.