Provided are methods for plastid genome editing and development of plants, plant cells, plant parts, and seeds comprising edited plastid genomes. Compositions for transformation of plastid genomes are further provided. Specifically, the plastid genome is modified to comprise the replacement of a targeted endogenous plastid genome sequence with a modified version of the target plastid sequence, where the modified plastid genome sequence has been designed to deliberately reduce its homology to the targeted endogenous plastid genome sequence and, in some cases, encode a protein containing one or more mutations.