This study aimed to prolong the raw buffalo milk handling and cold storage period by controlling the microbes, enhancing sensory properties and their functionality after supplementing bioactive peptides. The additions included hen and duck egg white protein isolates (HPI and DPI), pepper seed protein (PSP), and pepsin-kidney bean protein hydrolysate (PKH). Five milk treatments were prepared and evaluated as non-supplemented milk (M- Control), hen egg white protein isolate-supplemented milk (M-HPI), duck egg white protein isolate-supplemented milk (M-DPI), pepper seeds protein-supplemented milk (M-PSP), and kidney bean hydrolysate-supplemented milk (M-PKH). Pyrogallol, protocatechuic, catechin, benzoic and caffeine were the main phenolic compounds, Apignin-6-arabinose, naringin, hesperidin, naringenin, kaempferol 3–2-p-comaroyl were the dominant flavonoids in milk samples based on HPLC profile. During 30 days of cold storage, the antioxidant potential of peptides-supplemented milk samples was significantly decreased (p ≤ 0.05) as decrement of phenolic compounds and flavonoids; the pH was nearly stable, the titratable acidity and total soluble solids (TTS) were (p ≤ 0.05) raised. PSP and PKH were inhibited (p ≤ 0.05) the decay of sugars in M-PSP, and M-PKH by reducing 45% of bacterial load as compared to other milk samples. PSP was significantly (p ≤ 0.05) scavenged 87% of DPPḢ compared to other peptides. Besides, PSP followed by PKH reduced considerably (p ≤ 0.05) the growth of tested bacteria, molds, and yeasts. The PSP has significantly increased the whiteness of M-PSP as compared to other milk samples. M-PSP had the highest score in color, taste, and flavor, followed by M-PKH.