This OSF repository contains the lexical data, reproducible code, derived phylogenetic character matrices, analysis outputs, and supplementary materials associated with the study “A Phonology-Aware Phylogeny for Asia Minor Greek”. The study investigates the internal phylogenetic structure of Asia Minor Greek varieties by comparing different representations of historical linguistic signal. Three principal phylogenetic datasets are constructed: (i) binary cognate characters, (ii) recurrent sound-correspondence characters inferred from phonetic alignments of etymologically related forms using LingPy and LingRex, and (iii) a combined cognate and sound-correspondence matrix. Phylogenetic inference is conducted using Bayesian analysis in MrBayes. The repository documents the complete workflow from the comparative lexical database to the final phylogenetic analyses. It includes the cleaned input data, data-format specifications, preprocessing scripts, random seeds and software settings required for reproducibility, intermediate alignment and correspondence-pattern outputs, cognate and sound-correspondence character matrices, Bayesian tree files, and diagnostic outputs. Detailed information about the structure of the input data and instructions for reproducing the analyses is provided in `README.md`.