The thing to untangle first is that Zendesk is two products wearing one name: a ticket queue, and a whole support operating system of triggers, macros, SLAs, a help center, and bundled chat and phone. Some teams only use the queue; others shaped their whole process around the automation, and that decides your shortlist. If you want an integrated, multi-channel replacement, Chatwoot pulls website chat, email, and social messaging into one shared inbox and adds a help center and CSAT reporting. If a solid shared inbox over email is what you actually need, FreeScout is a lightweight, self-hosted help desk with no limits on agents, tickets, or mailboxes, and Zammad offers mature ticketing across email, chat, phone, and social with a REST API.
Expect the gaps to be in polish and administration, not core ticketing. Zendesk's marketplace integrations, report builders, and no-code admin controls are things support teams lean on heavily, and you will likely rebuild dashboards, re-create roles and permissions, and tune notification noise by hand. Budget for agent retraining too, because small workflow differences change triage speed and response quality more than the feature list suggests. Peppermint is worth knowing as the leaner end of the spectrum, a simpler markdown-based ticket system for teams that want a clean queue without the weight of a full suite.
Plan the migration around exports and APIs. Pull users, organizations, tickets, comments, tags, custom fields, attachments, and help center articles before you touch routing. Ticket bodies and timestamps usually survive, but automation history, satisfaction ratings, and some channel metadata may not, and triggers, macros, SLAs, and views have to be rebuilt rather than imported. Run a parallel period where new mail routes to the new system while you validate the historical data, and set SPF, DKIM, and DMARC so outbound replies land.