diff --git a/packages/vite/src/node/__tests__/config.spec.ts b/packages/vite/src/node/__tests__/config.spec.ts
index 891ebd1da169de..ee90fb50774f67 100644
--- a/packages/vite/src/node/__tests__/config.spec.ts
+++ b/packages/vite/src/node/__tests__/config.spec.ts
@@ -1696,8 +1696,8 @@ describe('loadConfigFromFile', () => {
       expect(messages).toMatchInlineSnapshot(`
         [
           "(!) Your Vite config uses features that are unsupported by \`configLoader: 'native'\`, which is planned to become the default in a future major version of Vite:
-          - \`__dirname\` (vite.config.js:3). Use \`import.meta.dirname\` instead
-          - \`__filename\` (vite.config.js:4). Use \`import.meta.filename\` instead
+          - \`__dirname\` (vite.config.js:3:29). Use \`import.meta.dirname\` instead
+          - \`__filename\` (vite.config.js:4:30). Use \`import.meta.filename\` instead
         Set \`VITE_CONFIG_NATIVE_IGNORE_WARNING=true\` to suppress this warning.",
         ]
       `)
@@ -1712,7 +1712,7 @@ describe('loadConfigFromFile', () => {
         expect(messages).toMatchInlineSnapshot(`
           [
             "(!) Your Vite config uses features that are unsupported by \`configLoader: 'native'\`, which is planned to become the default in a future major version of Vite:
-            - \`__dirname\` (vite.config.ts:10). Use \`import.meta.dirname\` instead
+            - \`__dirname\` (vite.config.ts:10:29). Use \`import.meta.dirname\` instead
           Set \`VITE_CONFIG_NATIVE_IGNORE_WARNING=true\` to suppress this warning.",
           ]
         `)
@@ -1724,7 +1724,7 @@ describe('loadConfigFromFile', () => {
       expect(messages).toMatchInlineSnapshot(`
         [
           "(!) Your Vite config uses features that are unsupported by \`configLoader: 'native'\`, which is planned to become the default in a future major version of Vite:
-          - import "./helper" without a file extension (vite.config.js:1). Add the file extension
+          - import "./helper" without a file extension (vite.config.js:1:23). Add the file extension
         Set \`VITE_CONFIG_NATIVE_IGNORE_WARNING=true\` to suppress this warning.",
         ]
       `)
@@ -1735,7 +1735,7 @@ describe('loadConfigFromFile', () => {
       expect(messages).toMatchInlineSnapshot(`
         [
           "(!) Your Vite config uses features that are unsupported by \`configLoader: 'native'\`, which is planned to become the default in a future major version of Vite:
-          - import "./plugins" resolves to a directory index (vite.config.js:1). Import the index file directly
+          - import "./plugins" resolves to a directory index (vite.config.js:1:25). Import the index file directly
         Set \`VITE_CONFIG_NATIVE_IGNORE_WARNING=true\` to suppress this warning.",
         ]
       `)
@@ -1746,7 +1746,7 @@ describe('loadConfigFromFile', () => {
       expect(messages).toMatchInlineSnapshot(`
         [
           "(!) Your Vite config uses features that are unsupported by \`configLoader: 'native'\`, which is planned to become the default in a future major version of Vite:
-          - JSON import "./data.json" without import attributes (vite.config.js:1). Add \`with { type: 'json' }\`
+          - JSON import "./data.json" without import attributes (vite.config.js:1:18). Add \`with { type: 'json' }\`
         Set \`VITE_CONFIG_NATIVE_IGNORE_WARNING=true\` to suppress this warning.",
         ]
       `)
@@ -1761,7 +1761,7 @@ describe('loadConfigFromFile', () => {
       expect(messages).toMatchInlineSnapshot(`
         [
           "(!) Your Vite config uses features that are unsupported by \`configLoader: 'native'\`, which is planned to become the default in a future major version of Vite:
-          - import "./foo" resolves to a JSON file (vite.config.js:1). Import it with a \`.json\` extension and \`with { type: 'json' }\`
+          - import "./foo" resolves to a JSON file (vite.config.js:1:18). Import it with a \`.json\` extension and \`with { type: 'json' }\`
         Set \`VITE_CONFIG_NATIVE_IGNORE_WARNING=true\` to suppress this warning.",
         ]
       `)
@@ -1783,7 +1783,7 @@ describe('loadConfigFromFile', () => {
       expect(messages).toMatchInlineSnapshot(`
         [
           "(!) Your Vite config uses features that are unsupported by \`configLoader: 'native'\`, which is planned to become the default in a future major version of Vite:
-          - \`__dirname\` (esm-helper.mjs:1). Use \`import.meta.dirname\` instead
+          - \`__dirname\` (esm-helper.mjs:1:35). Use \`import.meta.dirname\` instead
         Set \`VITE_CONFIG_NATIVE_IGNORE_WARNING=true\` to suppress this warning.",
         ]
       `)
@@ -1794,7 +1794,7 @@ describe('loadConfigFromFile', () => {
       expect(messages).toMatchInlineSnapshot(`
         [
           "(!) Your Vite config uses features that are unsupported by \`configLoader: 'native'\`, which is planned to become the default in a future major version of Vite:
-          - ESM syntax in a file loaded as CommonJS (vite.config.js:1). Use a \`.mjs\` extension or set \`"type": "module"\` in the closest package.json
+          - ESM syntax in a file loaded as CommonJS (vite.config.js:1:1). Use a \`.mjs\` extension or set \`"type": "module"\` in the closest package.json
         Set \`VITE_CONFIG_NATIVE_IGNORE_WARNING=true\` to suppress this warning.",
         ]
       `)
diff --git a/packages/vite/src/node/nativeConfigCompat.ts b/packages/vite/src/node/nativeConfigCompat.ts
index b2fc57040f295b..0ddbed3c46c948 100644
--- a/packages/vite/src/node/nativeConfigCompat.ts
+++ b/packages/vite/src/node/nativeConfigCompat.ts
@@ -179,7 +179,8 @@ function describeIncompatibility(
   item: NativeConfigIncompatibility,
   root: string,
 ): string {
-  const loc = `${normalizePath(path.relative(root, item.file))}:${item.line}`
+  // 1-based column so terminals can link `file:line:column` to the exact position
+  const loc = `${normalizePath(path.relative(root, item.file))}:${item.line}:${item.column + 1}`
   switch (item.type) {
     case 'dirname':
       return `\`__dirname\` (${loc}). Use \`import.meta.dirname\` instead`