Background: Holder pasteurization (HoP) is the recommended method of pasteurization for donor human milk (DHM). The aim of the present study was to compare nutritional and microbiological impact on DHM of a new technique of pasteurization based on technical changes of HoP. Methods: We analyzed milk samples from 25 donors. Each sample, derived from one breast milk expression, was subdivided into three aliquots according to pasteurization: The first was not pasteurized, the second pasteurized by HoP, and the third was pasteurized by modified HoP (MHoP). Each aliquot was assessed as to its microbiological and nutritional profile. Nutritional profile included calcium and triglycerides concentrations detected by spectrophotometry and amino acid levels assessed by high-performance liquid chromatography (HPLC). Results: Triglycerides were significantly lower in pasteurized, by both methods, than in not pasteurized aliquots, while calcium and amino acids concentration were similar. Microbiological profile did not differ between HoP and MHoP aliquots. Conclusions: HoP and MHoP seem to have similar efficacy in preserving some nutritional characteristics of DHM and to confer similar microbiological safety. MHoP is time-saving and potentially costs-effective when compared to HoP, and it is; therefore, potentially of more interest from a practical point of view. Further studies are needed to confirm these findings.