Abstract Nuclear transfer technologies, such as metaphase II spindle transfer (MII-ST), are being developed to overcome poor oocyte quality and prevent children from acquiring severe mitochondrial DNA (mtDNA) disease. However, it is unclear whether these technologies perturb gene expression; and mtDNA carryover can be reduced to minimal levels. Using our pig model, we isolated individual karyoplasts with limited mtDNA carryover (306 ± 49 copies) from mature oocytes. Firstly, we reintroduced the spindle into its original cytoplast (autologous), fertilised, and cultured the resultant embryos to the hatching blastocyst stage of development. Following RNA-seq, 64 genes were differentially expressed at FDR < 0.05; and 1327 genes at P < 0.05. Pathways associated with cell cycle and epigenetic regulation and genes associated with nuclear-mitochondrial interactions were upregulated whilst protein translation pathways were downregulated. We then transferred karyoplasts to third party cytoplasts (heterologous) and undertook mtDNA next generation sequencing of 2-cell to hatching blastocyst stage preimplantation embryos. Nine of 20 embryos possessed two mitochondrial genomes. Our outcomes show that autologous nuclear transfer alone significantly changes hatching blastocyst gene expression; very low levels of mtDNA carryover can be preferentially replicated during early development; and nuclear and mitochondrial synchrony has not been reestablished.