In this article, we describe how Phon, an open-source software program for the transcription and analysis of phonological data, can be applied to facilitate clinical phonological analyses. We begin with a summary of the types of analyses that are frequently used in the assessment and management of speech sound disorders. We then discuss challenges inherent to the transcription and analysis of clinical phonological data. For each challenge, we discuss solutions currently available within Phon and offer an outlook on future methodological and technical developments in the area of clinical phonology. This article includes a step-by-step introduction to Phon suitable for readers who lack previous experience with the software. We conclude with a discussion of data sharing and its vital role in advancing research and intervention practices in the area of speech development and disorders.