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If git clone works over HTTPS but fails over SSH, the repository is probably reachable; the SSH route is failing at a different layer. Check the SSH clone URL and the required git user, test authentication directly, verify that the selected key belongs to the account with repository access, then investigate host-key or port-22 errors. HTTPS success does not validate any of those SSH-specific conditions.
Why HTTPS can work while SSH fails
Git uses separate connection stacks for HTTPS and SSH. An HTTPS clone checks the repository path and the hosting service’s HTTPS authentication flow. An SSH clone must also parse an SSH-style URL, connect as the service’s SSH account, select a private key, complete public-key authentication, validate the server’s host key, and reach the SSH port. The authenticated account must then be authorized to read the repository.
A failure in any one of those stages can coexist with a completely successful HTTPS clone. The most useful troubleshooting method is therefore to identify the failing layer instead of repeatedly changing credentials or recreating the repository.
Use this diagnostic order
Work through the checks in this order. Each test narrows the problem without changing unrelated settings.
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- Read the SSH remote URL and confirm its SSH user and repository path.
- Run a direct SSH authentication test, first normally and then with verbose output.
- If authentication is rejected, verify the private key, its public-key registration, and agent or configuration selection.
- Do not switch to
sudoas a first fix; elevated and normal users have different key environments. - If authentication succeeds but cloning fails, check repository authorization, spelling, and deploy-key scope.
- For a host-key error, verify the presented fingerprint before changing
known_hosts. - For a timeout or refusal on port 22, test the hosting service’s supported SSH-over-443 endpoint.
1. Check the SSH clone URL and login user
Inspect the remote that Git is actually using
From the repository directory, display the configured remotes:
git remote -vCompare the SSH URL with the hosting service’s clone URL. A common GitHub form is:
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git@github.com:OWNER/REPO.gitAn equivalent URL using the explicit SSH scheme is:
ssh://git@github.com/OWNER/REPO.gitReplace OWNER and REPO with the exact owner and repository names. Check capitalization, punctuation, renamed repositories, and organization ownership. A URL copied from an HTTPS button is not automatically a valid SSH URL.
Use git as the SSH account
GitHub requires remote connections to use the git user. Your GitHub personal username belongs in account authorization, not as the SSH login in the URL. For example, ssh://alice@github.com/OWNER/REPO.git is not the normal GitHub form; use git@github.com instead.
If you need to replace an incorrect remote, set it explicitly:
git remote set-url origin git@github.com:OWNER/REPO.git
git remote -vDo not diagnose keys until this value is correct. A valid key offered to the wrong SSH user will still be rejected.
2. Test SSH independently of Git
Run the normal authentication probe
Test the host and account without attempting a repository operation:
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ssh -T git@github.comA successful result normally confirms authentication and notes that the account does not provide an interactive shell. That message is expected for Git hosting; shell access is not required for cloning.
Collect verbose connection details
If the probe fails, repeat it with verbose logging:
ssh -vT git@github.comRead the output from top to bottom. It shows the host and port selected, the SSH configuration files read, identity files considered, keys offered, and the final authentication result. The final lines are more useful than the first warning: they distinguish a network connection that never formed from a server that rejected a key.
For an alias or nonstandard configuration, test the exact host name used by the Git remote. A successful probe against one alias does not prove that another alias selects the same key or port.
3. Fix Permission denied (publickey)
This message means the server rejected the public-key authentication attempt. The usual causes are an absent private key, the wrong key being offered, a public key not registered with the intended account, or an incorrect SSH user.
Confirm that the private key exists
Inspect your SSH directory and identify the private key that should be used. The private key stays on the computer; only its matching public key is uploaded to the hosting account. Do not paste a private-key file into an account setting or send it to another person.
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ssh -i ~/.ssh/KEY-FILE -vT git@github.comReplace KEY-FILE with the actual private-key filename. If this command authenticates successfully while the plain ssh -T command does not, the key exists but automatic selection is wrong.
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Verify the matching public key is registered
Derive or locate the public key corresponding to the private key, then compare it with the key registered in the intended hosting account. GitHub’s SSH key setup requires adding the public key to the account before SSH Git operations can authenticate.
Make sure you are checking the account that should read this repository. Registering a key on a different personal account, organization account, or old account produces the same public-key denial even though the key itself is valid.
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Many SSH clients ask ssh-agent for keys. List identities currently loaded in the agent:
ssh-add -lIf the intended key is absent, load it in the current user session:
ssh-add ~/.ssh/KEY-FILERun the verbose probe again and confirm that the intended identity is offered. An agent containing several keys can also cause the wrong account’s key to be tried first; an explicit -i test or a host-specific IdentityFile setting removes that ambiguity.
Make key selection deterministic with SSH configuration
For multiple accounts, create separate host aliases in your SSH configuration and assign each alias a key. The pattern is:
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Host github-work
HostName github.com
User git
IdentityFile ~/.ssh/id_ed25519_work
IdentitiesOnly yesUse the alias in the Git remote:
git@github-work:WORK-OWNER/REPO.gitThen test the same alias:
ssh -vT git@github-workThe important rule is consistency: the alias, key, account, and repository authorization must all describe the same identity. Keep each private key tied to the account for which its public key was registered.
4. Do not use sudo to hide a key problem
Running sudo git clone changes the user context. The elevated user may have a different home directory, a different .ssh directory, a different agent socket, and no access to the key that works for your normal account. A key created for your regular user is not automatically available to the elevated user.
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Run Git and SSH as one consistent user and fix that user’s key configuration. If a system-level directory is required after cloning, perform only that separate file operation with the necessary privileges; do not use elevation as the authentication test.
5. Separate SSH authentication from repository authorization
When ssh -T succeeds but cloning fails
A successful SSH probe proves that the server accepted a key for an account. It does not prove that the account can read every repository. Recheck:
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- Membership or read permission for the authenticated account.
- Whether the repository was moved, renamed, made private, or deleted.
- Whether the key is a deploy key attached to a different repository.
Deploy keys are repository-scoped credentials. A key that works for one repository can be denied for another, even on the same host. A “repository not found” response can indicate either a nonexistent path or a real repository for which the authenticated account has no permission.
Confirm which account the key represents
With multiple accounts, compare the key selected by ssh -vT with the public key registered on the account that has repository access. If the host authenticates you successfully but the wrong account is selected, correct the alias or IdentityFile rather than generating more keys at random.
Retest the exact clone operation
After correcting authorization or the path, run the same command the user needs:
git clone git@github.com:OWNER/REPO.gitA direct SSH test and a clone use the same host authentication but differ in the repository request. This final retest confirms that both layers now work.
6. Handle “Host key verification failed” safely
Host-key verification protects you from connecting to an unexpected server. The error concerns the server’s identity, not your repository password or public key. It can appear after a legitimate host migration, a changed network route, a rebuilt machine, or a stale entry in known_hosts; it can also indicate interception.
Inspect the stored entry
Find entries for the host in your known-hosts files:
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ssh-keygen -F github.comFor an explicit port-443 host, inspect that host name as well:
ssh-keygen -F ssh.github.comReview the line and the fingerprint presented by the SSH error. Compare it with the hosting provider’s current, published host-key fingerprints through a trusted channel before accepting a change.
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Change an entry only after verification
Do not blindly delete known_hosts or accept a new fingerprint merely to make the command continue. If the provider confirms the change, remove only the matching stale entry and reconnect so the verified key can be stored. A targeted removal command is:
ssh-keygen -R github.comUse the equivalent bracketed host-and-port form when the conflict is specifically for a nonstandard port. Re-run the SSH test, check the displayed fingerprint, and accept it only when it matches the provider’s published value.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.7. Work around a blocked SSH port 22
Some firewalls and proxy networks refuse outbound SSH on TCP port 22. In that case, key configuration can be perfect while the connection times out or is refused before authentication begins.
Test GitHub’s SSH endpoint on port 443
GitHub documents an SSH-over-443 endpoint for networks that block port 22:
Do these 3 things before closing this tab:
1Repair Windows errors before they cause bigger problems2Fix the driver behind crashes, sound loss and screen glitches3Clear out junk files and repair common Windows errorsssh -T -p 443 git@ssh.github.comThe hostname is ssh.github.com, not github.com. A successful response confirms that the network can reach the alternate endpoint and that your key still authenticates.
Clone with an explicit port
Use the ssh:// form when specifying a port:
git clone ssh://git@ssh.github.com:443/OWNER/REPO.gitMake port 443 transparent to existing GitHub URLs
Add a host rule to your SSH configuration:
Host github.com
Hostname ssh.github.com
Port 443
User gitAfter saving it, keep using the normal-looking remote and retest:
ssh -T git@github.com
git clone git@github.com:OWNER/REPO.gitCorporate proxies can still interfere with SSH traffic even on port 443. This workaround is documented for GitHub.com; GitHub Enterprise Server does not support this particular endpoint, so enterprise administrators must provide an environment-specific route.
Error-to-action map
| Observed symptom | Most likely layer | Next action |
|---|---|---|
Permission denied (publickey) |
SSH user, key selection, agent, or account registration | Run ssh -vT; confirm git as the user, the private key, its loaded-agent state, and registration on the intended account. |
Host key verification failed |
known_hosts entry or changed server identity |
Inspect the matching entry and compare the presented fingerprint with the provider’s published fingerprint before modifying it. |
| Timeout or connection refused on port 22 | Firewall, proxy, or network route | Test the supported port-443 endpoint and configure ssh.github.com on port 443 if it succeeds. |
Repository not found after SSH authentication |
Repository path or authorization | Recheck owner and repository spelling, account access, and deploy-key scope. |
| Authentication works only for one account | Multiple keys or SSH configuration selection | Use verbose output, an explicit IdentityFile, or host aliases so each key maps to the intended account. |
Choose the remedy by failure layer
| Remedy | Scope | Security and portability considerations | Access needed |
|---|---|---|---|
Correct the SSH URL and git user |
One remote | Low risk; works across operating systems and clients | Local repository access |
| Register or select the correct key | One account, or all repositories using that account | Preserves key-based authentication; requires careful private-key handling | Account settings and local key access |
| Fix repository permission or deploy-key scope | One repository or organization | Authorization change; may require an owner or administrator | Repository or organization administration |
Verify and repair known_hosts |
One host entry on one machine | Highest caution: accepting an unverified key weakens server-identity protection | Local SSH configuration; provider fingerprint information |
| Use SSH over port 443 | All matching host connections on that machine | Retains SSH keys where supported; proxies may still block it | Local SSH configuration; enterprise support may differ |
| Use HTTPS as a fallback | One remote or workflow | Valid when network policy prevents SSH or the organization standardizes on HTTPS | HTTPS credentials or token policy |
What not to do
- Do not replace
git@github.comwith your personal username. - Do not upload or disclose a private-key file; only the public key belongs in an account setting.
- Do not keep generating keys without checking which identity SSH is offering.
- Do not run Git with
sudomerely because the normal user receives a key error. - Do not delete the entire
known_hostsfile or accept a changed host key without fingerprint verification. - Do not infer repository permission from a successful
ssh -Tresponse; test the repository path separately.
When HTTPS is the right fallback
HTTPS remains a legitimate solution if organizational policy disallows SSH, a proxy cannot pass SSH even on port 443, or the hosting service does not provide the alternate endpoint you need. Switching protocols does not repair SSH, but it can provide a supported workflow while an administrator addresses firewall rules, account authorization, or key policy. Keep the HTTPS remote only if its credential method meets your organization’s requirements.
Do these 3 things before closing this tab:
1Repair Windows errors before they cause bigger problems2Fix the driver behind crashes, sound loss and screen glitches3Clear out junk files and repair common Windows errorsFinal verification checklist
Before treating the problem as fixed, verify all of the following in one session:
Quick Recap
git remote -vshows the intended owner, repository, host, and SSH user.ssh -T(or the configured port-443 equivalent) authenticates the intended account.ssh -vTshows the expected identity file or agent key being offered.- The matching public key is registered to an account that can read the repository.
- No unverified host-key change remains in
known_hosts. - The exact
git clone, fetch, or pull command completes without a repository-not-found or authorization error.
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