diff --git a/.changeset/rotten-wombats-cry.md b/.changeset/rotten-wombats-cry.md
new file mode 100644
index 0000000000..d9817fbace
--- /dev/null
+++ b/.changeset/rotten-wombats-cry.md
@@ -0,0 +1,7 @@
+---
+"@redocly/cli": minor
+---
+
+Changed `lint` behavior with the `--generate-ignore-file` option.
+Now `lint` updates only the entries related to the file being linted.
+Other files' entries are unchanged.
diff --git a/docs/@v2/commands/lint.md b/docs/@v2/commands/lint.md
index 0135402116..5dd93dc239 100644
--- a/docs/@v2/commands/lint.md
+++ b/docs/@v2/commands/lint.md
@@ -352,7 +352,8 @@ This option is useful when you have an API design standard, but have some except
 It allows for highly granular control.
 
 {% admonition type="warning" %}
-This command overwrites an existing ignore file.
+This command updates ignore entries only for the API descriptions passed to the command.
+Existing entries for other API descriptions are preserved.
 {% /admonition %}
 
 The following command runs `lint` and adds all the errors to an ignore file:
@@ -369,6 +370,15 @@ Generated ignore file with 3 problems.
 
 The errors in the ignore file `.redocly.lint-ignore.yaml` are ignored when the `lint` command is run.
 
+If you run:
+
+```bash
+redocly lint api1.yaml --generate-ignore-file
+```
+
+Only the ignore entries related to api1.yaml are updated.
+Ignore entries for other API descriptions remain unchanged.
+
 To generate an ignore file for multiple API descriptions, pass them as arguments:
 
 ```bash
diff --git a/packages/cli/src/__tests__/commands/lint.test.ts b/packages/cli/src/__tests__/commands/lint.test.ts
index f91469d653..1106f38f0a 100644
--- a/packages/cli/src/__tests__/commands/lint.test.ts
+++ b/packages/cli/src/__tests__/commands/lint.test.ts
@@ -8,6 +8,7 @@ import {
   loadConfig,
 } from '@redocly/openapi-core';
 import { blue } from 'colorette';
+import { resolve } from 'node:path';
 import { performance } from 'perf_hooks';
 import { type MockInstance } from 'vitest';
 import { type Arguments } from 'yargs';
@@ -114,7 +115,7 @@ describe('handleLint', () => {
       );
     });
 
-    it('should call mergedConfig with clear ignore if `generate-ignore-file` argv', async () => {
+    it('should call forAlias when `generate-ignore-file` argv is set', async () => {
       await commandWrapper(handleLint)({ ...argvMock, 'generate-ignore-file': true });
       expect(configFixture.forAlias).toHaveBeenCalledWith(undefined);
     });
@@ -151,6 +152,64 @@ describe('handleLint', () => {
       expect(configFixture.skipPreprocessors).toHaveBeenCalledWith(['preprocessor']);
     });
 
+    it('should update only the linted file entries and preserve ignore entries for other files', async () => {
+      const barAbsRef = resolve('ignore-bar.yaml');
+      const fooAbsRef = resolve('ignore-foo.yaml');
+
+      configFixture.ignore = {
+        [barAbsRef]: {
+          'no-empty-servers': new Set(['#/servers']),
+          'operation-summary': new Set(['#/paths/~1items/get/summary']),
+        },
+        [fooAbsRef]: {
+          'no-empty-servers': new Set(['#/servers']),
+        },
+      };
+
+      vi.mocked(configFixture.clearIgnoreForRef).mockImplementation((ref: string) => {
+        const absRef = resolve(ref);
+        delete configFixture.ignore[absRef];
+      });
+
+      vi.mocked(configFixture.addIgnore).mockImplementation((problem: any) => {
+        const loc = problem.location[0];
+        if (loc.pointer === undefined) return;
+        const fileIgnore = (configFixture.ignore[loc.source.absoluteRef] =
+          configFixture.ignore[loc.source.absoluteRef] || {});
+        const ruleIgnore = (fileIgnore[problem.ruleId] = fileIgnore[problem.ruleId] || new Set());
+        ruleIgnore.add(loc.pointer);
+      });
+
+      vi.mocked(lint).mockResolvedValueOnce([
+        {
+          ruleId: 'no-empty-servers',
+          severity: 1,
+          message: 'Servers must not be empty',
+          location: [{ source: { absoluteRef: barAbsRef }, pointer: '#/servers' }],
+          suggest: [],
+          ignored: false,
+        } as any,
+      ]);
+
+      await commandWrapper(handleLint)({
+        ...argvMock,
+        apis: ['ignore-bar.yaml'],
+        'generate-ignore-file': true,
+      });
+
+      expect(configFixture.ignore[fooAbsRef]).toEqual({
+        'no-empty-servers': new Set(['#/servers']),
+      });
+
+      expect(configFixture.ignore[barAbsRef]).toEqual({
+        'no-empty-servers': new Set(['#/servers']),
+      });
+
+      expect(configFixture.saveIgnore).toHaveBeenCalled();
+
+      configFixture.ignore = {};
+    });
+
     it('should call formatProblems and getExecutionTime with argv', async () => {
       vi.mocked(lint).mockResolvedValueOnce(['problem'] as any);
       await commandWrapper(handleLint)({ ...argvMock, 'max-problems': 2, format: 'stylish' });
diff --git a/packages/cli/src/__tests__/fixtures/config.ts b/packages/cli/src/__tests__/fixtures/config.ts
index bf22eaa163..2611e20238 100644
--- a/packages/cli/src/__tests__/fixtures/config.ts
+++ b/packages/cli/src/__tests__/fixtures/config.ts
@@ -11,6 +11,7 @@ export const configFixture: Config = {
   },
   configPath: undefined,
   addIgnore: vi.fn(),
+  clearIgnoreForRef: vi.fn(),
   skipRules: vi.fn(),
   skipPreprocessors: vi.fn(),
   saveIgnore: vi.fn(),
diff --git a/packages/cli/src/commands/lint.ts b/packages/cli/src/commands/lint.ts
index 1ecf062c03..d0dc4a5c63 100644
--- a/packages/cli/src/commands/lint.ts
+++ b/packages/cli/src/commands/lint.ts
@@ -51,9 +51,6 @@ export async function handleLint({
     exitWithError('No APIs were provided.');
   }
 
-  if (argv['generate-ignore-file']) {
-    config.ignore = {}; // clear ignore
-  }
   const totals: Totals = { errors: 0, warnings: 0, ignored: 0 };
   let totalIgnored = 0;
 
@@ -95,6 +92,7 @@ export async function handleLint({
       totals.ignored += fileTotals.ignored;
 
       if (argv['generate-ignore-file']) {
+        config.clearIgnoreForRef(path);
         for (const m of results) {
           config.addIgnore(m);
           totalIgnored++;
@@ -118,9 +116,7 @@ export async function handleLint({
 
   if (argv['generate-ignore-file']) {
     config.saveIgnore();
-    logger.info(
-      `Generated ignore file with ${totalIgnored} ${pluralize('problem', totalIgnored)}.\n\n`
-    );
+    logger.info(`Explicitly ignored ${totalIgnored} ${pluralize('problem', totalIgnored)}.\n\n`);
   } else {
     printLintTotals(totals, apis.length);
   }
diff --git a/packages/core/src/config/config.ts b/packages/core/src/config/config.ts
index 837525353f..7ef6647bbe 100755
--- a/packages/core/src/config/config.ts
+++ b/packages/core/src/config/config.ts
@@ -166,6 +166,12 @@ export class Config {
     );
   }
 
+  clearIgnoreForRef(ref: string) {
+    const dir = this.configPath ? path.dirname(this.configPath) : process.cwd();
+    const absRef = isAbsoluteUrl(ref) ? ref : path.resolve(dir, ref);
+    delete this.ignore[absRef];
+  }
+
   saveIgnore() {
     const dir = this.configPath ? path.dirname(this.configPath) : process.cwd();
     const ignoreFile = path.join(dir, IGNORE_FILE);