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Most MySQL Workbench connection failures to a VPS occur in one of three layers: the network path never reaches the server, MySQL is listening only locally (or not running), or MySQL rejects the account after the connection arrives. Start by identifying the error, then test the exact address and port you entered in Workbench.
Use Standard TCP/IP when the VPS and its firewalls intentionally expose MySQL to your workstation. Use Standard TCP/IP over SSH when MySQL should remain private on the VPS. Classic MySQL normally uses TCP port 3306; Workbench’s SSH transport normally uses TCP port 22 to reach the VPS and then connects to MySQL through the tunnel.
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Workbench has two separate connection methods. They require different network rules, different fields and different diagnoses. Decide which design you actually want before changing MySQL configuration.
| Workbench method | What Workbench connects to | Required server-side access | When it fits |
|---|---|---|---|
| Standard TCP/IP | MySQL hostname or IP and MySQL port | MySQL must listen on a reachable interface; TCP 3306 (unless changed) must be allowed through the VPS firewall and cloud security group | A controlled private network or a deliberately restricted direct connection |
| Standard TCP/IP over SSH | SSH service on the VPS, then the MySQL listener from the VPS side of the tunnel | SSH access, normally TCP 22; MySQL can remain bound to localhost and need not be exposed publicly | The safer default when only administrators need database access |
For direct TCP/IP, Workbench asks for the server address, MySQL port, username and password. SSH mode adds the SSH hostname, SSH user and password or private-key fields, while the MySQL side uses the listener as seen from the VPS.
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Do not mix the two paths while testing. A successful SSH connection proves that the VPS and its local MySQL service are reachable through the tunnel; it does not prove that a public 3306 rule, public listener or direct-login account is correctly configured. Conversely, a working direct connection says nothing about whether your SSH key, SSH username or host-key record is correct.
Read the error as a layer diagnosis
- DNS failure or timeout: investigate the name, route, source address, firewall and cloud security group before changing MySQL users.
- Connection refused: the address is reachable, but no service is accepting that port. Check whether
mysqldis running, whether TCP networking is disabled, and which address it is bound to. - Host is not allowed: MySQL received the connection but found no account whose Host value matches the client.
- Access denied: the TCP path worked; check the username, password, authentication account and required schema privileges.
- Direct TCP fails but SSH works: the database is reachable from the VPS but the public exposure path is blocked or intentionally absent. Keeping the SSH design is often preferable.
This order prevents a common mistake: changing grants when packets never reached MySQL, or opening a firewall when the account password is the real problem. Record the exact Workbench message, hostname, resolved address, port and connection method before making a change so that you can tell which change fixed the issue.
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1. Enter a reachable VPS address, not an assumed localhost
In the Workbench connection dialog, choose Standard TCP/IP. Enter the VPS public address if your workstation reaches it over the internet, or its private address if both systems share a reachable private network. Enter the MySQL listener port, which is 3306 unless the server administrator changed it.
Do not enter localhost merely because MySQL runs on the VPS. In Workbench, localhost can resolve to 127.0.0.1 or ::1; that points to the computer running Workbench, not automatically to the VPS. It can also select a different MySQL account because MySQL matches both username and host.
Use the address that is actually routable from the workstation. A private VPS address may work only when you are on the provider’s private network, a site-to-site VPN or another permitted network. A public address may resolve correctly but still be filtered by a provider security group. If the hostname has both IPv4 and IPv6 records, make sure the selected address family is reachable and that MySQL is listening on that family; a working IPv4 rule does not automatically make an IPv6 attempt work.
Check for simple transcription errors as well: an old VPS address after a rebuild, a custom DNS record pointing to another machine, a changed non-default MySQL port, or an SSH port accidentally entered in the MySQL field. The SSH port belongs in the SSH connection settings, not in the direct MySQL port field.
2. Confirm that MySQL is running and listening
On the VPS, verify the MySQL service status using the service manager provided by its operating system. If the service is stopped, start it and inspect its log for configuration or storage errors. Then inspect listening sockets with the platform’s socket tool, such as ss -lntp, and confirm that the MySQL process owns the expected port.
A listener on 127.0.0.1:3306 accepts only connections originating locally on the VPS. A listener on a specific VPS interface accepts connections arriving through that interface. If no TCP socket exists, inspect the effective MySQL settings rather than assuming the default port.
Check the exact port shown by the socket listing against the port saved in Workbench. A service can be healthy while listening on a custom port, and Workbench will report a failure if it continues trying 3306. Also distinguish a Unix socket from a TCP listener: local command-line clients may work through a socket even when TCP/IP is unavailable.
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3. Check bind_address and skip_networking
MySQL’s bind_address determines which network interfaces accept TCP/IP connections. When it is set to 127.0.0.1, MySQL listens only on the loopback interface and cannot accept a direct remote connection. A wildcard setting listens on more interfaces and therefore creates broader exposure. Where direct access is required, bind to the specific VPS address or interface needed by the application and administrators.
The skip_networking option disables TCP/IP networking entirely. If it is enabled, a TCP test to any address or port will fail even when local socket connections work.
Inspect the effective values from a local administrative session:
SHOW VARIABLES LIKE 'bind_address';
SHOW VARIABLES LIKE 'skip_networking';
SHOW VARIABLES LIKE 'port';After changing configuration, restart or reload MySQL according to the setting’s requirements, then verify the listening socket again. A configuration edit alone does not prove that the running process adopted the new value. Confirm the new listener before opening a firewall rule; otherwise you may expose a port that still has no service behind it.
When choosing a bind address, use the interface through which approved clients arrive. Binding to one specific private address is narrower than binding to every interface. If the VPS has several addresses, selecting the wrong one can make the service appear healthy locally while the intended network path receives a refusal or timeout.
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4. Open every required firewall layer
Direct access requires permission at each network boundary:
- Permit TCP 3306 (or the configured MySQL port) in the VPS operating-system firewall.
- Permit the same port in the hosting provider’s cloud firewall or security group.
- Restrict the source to the workstation’s public address or to the required private subnet, rather than allowing every internet address.
- Check intermediate corporate, home or VPN firewalls if the workstation is on a managed network.
For SSH tunneling, allow SSH, normally TCP 22, to the VPS. MySQL does not need to be open to the workstation’s public address because the tunnel carries the database connection through SSH; the VPS must still be able to reach its own MySQL listener.
Use a port test from the workstation to the exact address and port entered in Workbench. A timeout usually means filtering or routing; a refusal usually means the host answered but no process is listening there. A successful port test does not validate MySQL credentials, so continue with account checks.
Remember that the source address seen by the VPS may not be the workstation’s local address. Network address translation, a VPN gateway or a corporate egress proxy can change it. Allow the actual egress address shown by the server-side connection logs or network records, and update the rule when that address legitimately changes. Do not solve a temporary address mismatch by opening the port to every source.
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5. Match the MySQL account to the client host
MySQL accounts are identified by a pair: User and Host. A password can be correct while login fails if the account’s Host value does not match the workstation as MySQL sees it.
For example, an account such as 'appuser'@'198.51.100.25' is different from 'appuser'@'localhost'. The first permits a connection from that client address; the second is for a local connection on the database server. If the workstation’s source address changes because of a VPN, NAT or dynamic ISP address, the previously matching account may no longer apply.
Use an administrative connection on the VPS to inspect existing definitions:
SELECT User, Host FROM mysql.user WHERE User = 'appuser';Inspect the account that matches the actual source, not merely the account with the same username. A local test using localhost can select a different row from a remote test using an IP address, which explains why “the password works on the server” is not conclusive.
Create or alter an account for the actual, controlled source address and grant only the required schema privileges. A typical pattern is:
CREATE USER 'appuser'@'198.51.100.25' IDENTIFIED BY 'use-a-strong-secret';
GRANT SELECT, INSERT, UPDATE, DELETE ON db_name.* TO 'appuser'@'198.51.100.25';Adjust the privileges to the application or administrative task. Do not leave a broad '%' Host rule when a specific source address or subnet is known; a wildcard can make the account usable from any host that can reach MySQL. If a subnet is necessary, define the narrowest supported host pattern and pair it with an equally narrow firewall rule.
Granting access to db_name.* does not automatically grant access to every schema, and successful authentication does not guarantee permission to open the database or run a particular statement. Ask for only the operations needed by the Workbench user. If an account already exists, alter its password or grants deliberately rather than creating several similarly named accounts that make host matching harder to audit.
Use Workbench’s SSH tunnel when MySQL should stay private
SSH tunneling avoids exposing a public MySQL listener. MySQL may remain bound to 127.0.0.1; Workbench logs in to the VPS over SSH and forwards the database connection from there. This separates two authentication steps: SSH proves that you may reach the VPS, and MySQL then authenticates the database user.
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- Set SSH Hostname to the VPS address and include a non-default SSH port if the server uses one.
- Enter the SSH username. Select the OpenSSH private-key file, or provide an SSH password if that is the server’s permitted authentication method.
- For the MySQL section, set the hostname to the listener as seen from the VPS, commonly
127.0.0.1, and set the MySQL port to its local listening port. - Enter the MySQL username and password separately from the SSH credentials.
- When Workbench presents an SSH host-key fingerprint, verify it against a trusted record for the VPS. Treat an unexpected changed fingerprint as a security event and investigate it outside the connection dialog.
- Test the connection. The workstation needs SSH reachability; it does not need direct TCP 3306 reachability.
Workbench uses OpenSSH key files for this method. If your existing private key is a PuTTY .ppk file, convert it to OpenSSH format before selecting it. Keep the converted key protected with appropriate filesystem permissions.
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The MySQL hostname in the SSH section is relative to the VPS, not to your workstation. Therefore 127.0.0.1 means the VPS loopback interface in this context. If MySQL listens on a private VPS address instead, use that address as seen from the VPS. A common mistake is to enter the VPS public address as the MySQL-side host and then troubleshoot a route that the tunnel does not need.
SSH tunneling still depends on the VPS’s local MySQL service, port and account. If the local listener is down, skip_networking is enabled or the MySQL credentials are wrong, SSH authentication can succeed while the Workbench database test fails. Diagnose the two stages separately.
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Direct TCP/IP versus SSH tunneling
| Consideration | Direct TCP/IP | SSH tunnel |
|---|---|---|
| Public exposure | MySQL port is reachable wherever firewall rules permit it | Only SSH is exposed; MySQL can stay local to the VPS |
| Firewall work | Allow MySQL at both the VPS and cloud layers, ideally from one source address | Allow SSH; no public MySQL rule is required |
| MySQL bind setting | Must include the destination interface | Can remain on localhost if SSH forwards to it |
| Credentials | MySQL credentials travel over the MySQL TCP session | SSH credentials and MySQL credentials are separate |
| Operational reachability | Useful for applications or networks that need native database TCP access | Useful for administrator access from a workstation without widening database exposure |
| Failure surface | DNS, routing, two firewall layers, listener and account matching all matter | SSH DNS, routing, firewall, key or password, tunnel target, listener and MySQL account matter |
Choose direct TCP when an application or approved private network genuinely needs native database connectivity and you can enforce a narrow source rule. Choose SSH when the users are administrators on workstations and there is no operational reason to publish MySQL. SSH does not remove the need for strong MySQL credentials or least-privilege grants; it reduces the number of systems that can reach the database port directly.
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Workbench reports a timeout
Resolve the VPS hostname from the workstation and confirm it resolves to the intended address. Test the selected port, then inspect cloud security-group rules, the VPS firewall and any network ACLs. Confirm that the source address allowed by the rule is the workstation’s actual egress address, not an old home or VPN address. If SSH mode times out, test port 22 rather than 3306 and verify the SSH hostname and custom SSH port.
Workbench reports “connection refused”
Check that mysqld is running and listening on the port you entered. Then check bind_address and skip_networking. A service bound only to loopback will refuse or fail to accept a connection aimed at the VPS’s external address. A refusal on the SSH port is a separate problem from a refusal on the MySQL port.
Workbench reports “host is not allowed”
The network path reached MySQL, but no account has a matching Host value. Determine the client’s source address as seen by the server, then create or grant the least-privileged account for that host or approved subnet. Check that you are not testing with a username that exists only as 'user'@'localhost'.
Workbench reports “access denied”
Verify that you selected the intended MySQL username, that its password is current, and that the account has privileges on the requested schema. An account can authenticate successfully and still lack permission to use a particular database. In SSH mode, confirm that you did not accidentally enter the SSH username where the MySQL username belongs.
Direct TCP fails but SSH works
This usually means MySQL is healthy on the VPS while the direct exposure path is blocked, filtered or intentionally disabled. Keep the SSH method if it meets the operational need. If direct access is genuinely required, correct the listener interface and both firewall layers, then restrict the source as tightly as possible. Do not loosen the firewall simply because tunneling works.
Workbench warns about an SSH host-key change
Do not bypass the warning automatically. Verify the VPS fingerprint through a trusted administrative channel. A changed key can result from a legitimate rebuild, but it can also indicate that you are connecting to a different host or that the connection is being intercepted. Handle the known-host record outside the connection dialog after the identity is confirmed.
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A local MySQL client works but Workbench does not
Determine whether the local client used a Unix socket, localhost, a different port or a different MySQL account. Repeat the test with TCP and the same address, port and username that Workbench uses. Matching the transport and account removes misleading differences between a local success and a remote failure.
Security checklist before enabling remote access
- Prefer a private network or SSH tunnel when only administrators need access.
- If direct TCP is necessary, bind MySQL to the specific required interface rather than every interface.
- Permit the MySQL port only from known source addresses in both the VPS firewall and cloud security group.
- Use a MySQL account whose Host value matches that source and grant only the required schema privileges.
- Keep SSH host-key verification enabled and protect private-key files.
- Document the configured MySQL port if it differs from 3306; changing the port alone is not a substitute for source restriction.
- After every change, retest in order: listener, network port, Workbench transport, then MySQL authentication and privileges.
- Remove temporary broad firewall rules and test accounts after troubleshooting.
- Record the selected bind address, port, approved source and account Host value so future administrators do not reopen the wrong interface.
Provider-specific firewall commands and pricing vary by distribution and hosting platform. The material decisions are independent of the provider: which interface MySQL listens on, which source may reach it, whether SSH is the transport, and which MySQL account Host and privileges are required.
Frequently Asked Questions
Should I enter the VPS IP address or localhost in MySQL Workbench?
For Standard TCP/IP, enter the VPS public or reachable private address. Use localhost only when Workbench is running on the VPS itself. In Standard TCP/IP over SSH, localhost or 127.0.0.1 in the MySQL section refers to the VPS side of the tunnel.
Do I need to open port 3306?
Only for direct TCP/IP access. Permit TCP 3306, or the configured MySQL port, in both the VPS firewall and cloud security group, restricted to the needed source. SSH tunneling normally requires only SSH, usually TCP 22, to be reachable from your workstation.
Why does SSH tunneling work when direct TCP/IP does not?
The tunnel reaches MySQL from the VPS itself, so MySQL may remain bound to 127.0.0.1 and port 3306 need not be publicly exposed. Direct TCP additionally requires a suitable bind address, route and firewall permission at every network layer.
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Why do I get access denied after the port is open?
An open port proves only that the TCP path reached MySQL. Check the username, password, requested schema and the account’s Host value. MySQL treats, for example, ‘appuser’@’localhost’ and ‘appuser’@’198.51.100.25’ as different accounts.
Can I leave bind_address set to 127.0.0.1?
Yes, when you use Workbench’s SSH method and the tunnel connects to the VPS loopback listener. No, for direct remote TCP/IP; bind_address must include the interface through which the client connects.
What does skip_networking do?
It disables MySQL TCP/IP networking. Local socket connections may still work, but neither direct Workbench TCP/IP nor the MySQL side of an SSH tunnel can connect through TCP while it is enabled.
Do I need to convert a PuTTY key for Workbench SSH?
Yes. Workbench’s SSH method expects an OpenSSH private-key file. Convert a PuTTY .ppk key to OpenSSH format, protect the converted file, and select it in the SSH settings.
Is allowing ‘appuser’@’%’ a good fix?
It can make host matching succeed, but it permits the account from any host that can reach MySQL. Prefer the narrowest known source address or subnet and enforce the same restriction in the firewall.
What should I do when Workbench reports a changed SSH fingerprint?
Pause and verify the VPS fingerprint through a trusted channel. A rebuild can legitimately change a key, but an unexpected change can also mean the hostname points elsewhere or the connection is being intercepted. Update the known-host record only after verification.
The Bottom Line
Classify the error first, then verify the exact address and port, the MySQL listener and bind settings, every firewall layer, and finally the account’s User/Host match and grants. Use direct TCP/IP only with tightly restricted exposure; otherwise select Standard TCP/IP over SSH, keep MySQL private on the VPS, and authenticate separately to SSH and MySQL.
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