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Raw goat milk was treated with a continuous mode of pulsed electric field (PEF) system, at three levels of field strength (20, 30, and 40 kV/cm) with monopolar square‐wave pulses of 5 and 10 µs treatment time. The physicochemical properties, particle size distribution, fatty acid profiling, and metal migrations of untreated and PEF‐treated goat milk were evaluated. The results indicated that PEF‐treated goat milk (40 kV/cm; 10 µs) had significant changes (p <.05) in pH and titratable acidity value of the samples due to the decrease in calcium ion (Ca2+), which leads to the protonation of the phosphate. The specific surface area (SSA) value significantly increased (p <.05) with the increase of PEF treatment time. PEF treatment was shown to reduce (p <.05) the total saturated fatty acids (∑SFAs) and total polyunsaturated fatty acids (∑PUFAs) of goat milk, while total monounsaturated fatty acids (∑MUFAs) were increased. The disintegration of fat and triacylglycerol breakdown from the fat globule (FG) membrane, together with heterogeneous metal catalysis oxidation may have caused the degradation of certain fatty acids (p <.05) in the study. Mean concentrations of micro‐elements (Fe, Cr, Mn, and Ni) in all PEF‐treated samples were within the permissible limit of heavy metals according to the USFDA drinking water quality standard. Practical applications: PEF is an emerging alternative pasteurizing method, when applied correctly could prolong the shelf‐life, while lessening the detrimental impacts on the organoleptic properties of goat milk. The results show that pasteurization via monopolar PEF can be recommended to enhance the quality of goat milk at the industry level. [ABSTRACT FROM AUTHOR]