Bioactive peptides (BPs) content of dairy products is suggested to be a significant ingredient for reducing breast cancer (BC) risk. There is no observational study regarding the correlation between BPs and the risk of chronic disease because BPs' content of food items has not been evaluated in any study. The goal of the current study was to assess the association of dairy-originated BPs with BC risk. One hundred thirty-four women with BC and 267 cancer-free controls were selected from referral hospitals in Tehran, Iran. The development of an in-silico model for estimation of the bioactive and digestion-resistant peptides content of dairy products was done in our previous research. The risk assessment for BPs and BC association was performed across the tertiles of the peptide's intake. Odds ratios (OR) were calculated by logistic regression. The negative association of all bioactive and digestion-resistant peptides except for peptides with high hydrophilicity and low bioactivity was seen in all models. In PR-negative subjects only the association of total dairy intake (OR: 0.61; 95% CI: 0.26-1.45; P for trend: 0.276), peptides with low bioactivity (OR: 0.40; 95% CI: 0.16-1.02; P for trend: 0.0.052), antidiabetic peptides (OR: 0.42; 95% CI: 0.17-1.05; P for trend: 0.0.062) and di-peptides (OR: 0.42; 95% CI: 0.17-1.05; P for trend: 0.0.062) were not significant in the final model. Also, no significant association between ER-negative subjects and total dairy intake (OR: 0.41; 95% CI: 0.16-1.07; P for trend: 0.0.068) was noted. Our findings deduced that milk-derived BPs negatively associate with the risk of ER/PR/HER2 negative BC among Iranian women.Supplemental data for this article is available online at https://doi.org/10.1080/01635581.2021.2009884.