The objective of this study was to evaluate and provide further insights into how dairy cows genetically divergent for milk urea N breeding values [MUNBV, high (2.21 ± 0.21) vs. low (1.16 ± 0.21); µ ± SEM], consuming either fresh cut Plantain (Plantago lanceolata L., PL) or Ryegrass (Lolium perenne L., RG) herbage, impacted the nutraceutical profile of whole milk by investigating amino and fatty acid composition and applying metabolomic profiling techniques. Both diet and MUNBV, and their interaction term, were found to affect the relative abundance of alanine, glycine, histidine, and phenylalanine in the milk (p < 0.05), but their minor absolute differences (up to ~0.13%) would not be considered biologically relevant. Differences were also detected in the fatty acid profile based on MUNBV and diet (p < 0.05) with low MUNBV cows having a greater content of total unsaturated fatty acids (+16%) compared to high MUNBV cows and cows consuming PL having greater content of polyunsaturated fatty acids (+92%), omega 3 (+101%) and 6 (+113%) compared to RG. Differences in the metabolomic profile of the milk were also detected for both MUNBV and dietary treatments. Low MUNBV cows were found to have greater abundances of choline phosphate, phosphorylethanolamine, N-acetylglucosamine 1-phosphate, and 2-dimethylaminoethanol (p < 0.05). High MUNBV cows had a greater abundance of methionine sulfoxide, malate, 1,5-anhydroglucitol (1,5-AG), glycerate, arabitol/xylitol, 3-hydroxy-3-methylglutarate, 5-hydroxylysine and cystine (p < 0.05). Large differences (p < 0.05) were also detected as a result of diet with PL diets having greater abundances of the phytochemicals 4-acetylcatechol sulfate, 4-methylcatechol sulfate, and p-cresol glucuronide whilst RG diets had greater abundances of 2,6-dihydroxybenzoic acid, 2-acetamidophenol sulfate, and 2-hydroxyhippurate. The results of this study indicate the potential to alter the nutraceutical value of milk from dietary and genetic strategies that have been previously demonstrated to reduce environmental impact.