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 in PRIDE consists of quantitative proteomic profiles of mouse ovarian samples and oocytes from the experimental 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. The dataset was generated to characterize protein abundance changes and identify molecular pathways associated with L-Phe-mediated regulation of ovarian and reproductive functions.