Purpose: Smoothed cepstral peak prominence (CPPS) and harmonics-to-noise ratio (HNR) are acoustic measures related to the periodicity, harmonicity, and noise components of an acoustic signal. To date, there is little evidence about the advantages of CPPS over HNR in voice diagnostics. Recent studies indicate that voice fundamental frequency (F0) and intensity (sound pressure level [SPL]), sample duration (DUR), vowel context (speech vs. sustained phonation), and syllable stress (SS) may influence CPPS and HNR results. The scope of this work was to investigate the effects of voice F0 and SPL, DUR, SS, and token on CPPS and HNR in dysphonic voices. Method: In this retrospective study, 27 Brazilian Portuguese speakers with voice disorders were investigated. Recordings of sustained vowels (SVs) /a:/ and manually extracted vowels (EVs) /a/ from Consensus Auditory-Perceptual Evaluation of Voice sentences were acoustically analyzed with the Praat program. Results: There was a highly significant effect of F0, SPL, and DUR on both CPPS and HNR (p < 0.001), whereas SS and vowel context significantly affected CPPS only (p < 0.05). Higher SPL, F0, and lower DUR were related to higher CPPS and HNR. SVs moderately-to-highly correlated with EVs for CPPS, whereas HNR had few and moderate correlations. In addition, CPPS and HNR highly correlated in SVs and seven EVs (p < 0.05). Conclusion: Speaking prosodic variations of F0, SPL, and DUR influenced both CPPS and HNR measures and led to acoustic differences between sustained and excised vowels, especially in CPPS. Vowel context, prosodic factors, and token type should be controlled for in clinical acoustic voice assessment.