DWI is an important contrast for prostate MRI to enable early and accurate detection of cancer. This study introduces a Dixon 3-shot-EPI protocol with structured low-rank reconstruction for navigator-free DWI. The aim is to overcome the limitations of single-shot EPI (ssh-EPI), such as geometric distortions and fat signal interference, while addressing the motion-induced phase variations of multishot EPI and simultaneously allowing water/fat separation. DWI data were acquired from 7 healthy volunteers using both Dixon 3-shot EPI and standard fat-suppressed ssh-EPI with similar scan times for comparison. Two readers evaluated image quality using a 5-point Likert scale regarding different aspects. The ADC values were quantitatively compared between protocols. To show feasibility in a clinical setting, the protocol was applied to two patients. From the reader scores, Dixon 3-shot EPI significantly reduced geometric distortion compared with ssh-EPI (p < 0.01), with no significant differences in edge definition, SNR, or overall image quality. There was no significant difference in ADC values between the two protocols. However, the Dixon multishot-EPI protocol offered advantages such as self-referenced B0 map-driven distortion correction, greater flexibility in imaging parameters, and superior fat suppression. In the patient data, the lesion could be clearly identified in both protocols and on the associated ADC maps. The proposed Dixon 3-shot-EPI protocol shows promise as an alternative to ssh-EPI for prostate DWI, providing reduced geometric distortions and improved fat suppression. It addresses common DWI issues based on EPI and enhances scanning flexibility, indicating potential for optimized imaging.