The key difference is what you want your support system to optimize for. Zendesk and Intercom offer mature workflows, integrations, reporting, and proven processes. AI-native help desks build AI into the workflow from the start, with the potential to resolve issues, take actions, summarize context, route conversations, and reduce repetitive work. The real test is not the AI demo but resolution rates, escalation quality, agent workload, and time saved. Mature teams may prefer Zendesk or Intercom, while smaller teams starting fresh may benefit more from an AI first approach.