Atypical prosody in speech production is a core feature of Autism Spectrum Disorder (ASD) that can impact everyday life communication. Because the ability to modulate prosody develops around the age of speech acquisition, it might be affected by ASD symptoms and developmental delays that emerge at the same period. Here, we investigated the existence of a prosodic signature of developmental level and ASD symptom severity in a sample of 74 autistic preschoolers. We first developed an original diarization pipeline to extract preschoolers’ vocalizations from recordings of naturalistic social interactions. Using this novel approach, we then found a robust voice quality signature of ASD developmental difficulties in preschoolers. Furthermore, some prosodic measures were associated with one year later outcome in participants who had not acquired speech yet. Altogether, our results highlight the potential benefits of automatized diarization algorithms and prosodic metrics for digital phenotyping in psychiatry, helping clinicians establish early diagnosis and prognosis.