This study investigated the molecular mechanisms underlying the regulation of female reproduction by Lactobacillus johnsonii-associated L-phenylalanine (L-Phe). Multiple omics approaches were used to characterize metabolic and molecular alterations associated with reproductive regulation. The proteomic dataset deposited here consists of quantitative proteomic profiles of mouse ovarian tissues from control and L-phenylalanine-treated groups. Data-independent acquisition (DIA) mass spectrometry was used for quantitative proteomic analysis, while data-dependent acquisition (DDA) data generated from pooled and fractionated peptide samples were used for spectral library construction during the original analysis workflow. The dataset was generated to characterize protein abundance changes and identify molecular pathways associated with L-Phe-mediated regulation of ovarian and reproductive functions. A companion mouse oocyte proteomics dataset from the same study is available in PRIDE under accession PXD083329.