To handle incoming WhatsApp audio messages in a Go application using Twilio and AssemblyAI, users need to create a new project, install the required dependencies, store their credentials as environment variables, retrieve the necessary credentials, set up the application logic, connect the app to the Twilio WhatsApp Sandbox, start the application, set up a Twilio WhatsApp Webhook, test the application, and learn how to use these tools for automated transcription services or voice-driven data collection platforms.