diff --git a/packages/cli/src/ui/AppContainer.tsx b/packages/cli/src/ui/AppContainer.tsx
index 426543d772..ae0f43b418 100644
--- a/packages/cli/src/ui/AppContainer.tsx
+++ b/packages/cli/src/ui/AppContainer.tsx
@@ -590,7 +590,7 @@ Logging in with Google... Please restart Gemini CLI to continue.
         },
         Date.now(),
       );
-      console.error('Error refreshing memory:', error);
+      debugLogger.warn('Error refreshing memory:', error);
     }
   }, [config, historyManager, settings.merged]);
 
diff --git a/packages/core/src/tools/glob.ts b/packages/core/src/tools/glob.ts
index 0dbd71e479..f090056654 100644
--- a/packages/core/src/tools/glob.ts
+++ b/packages/core/src/tools/glob.ts
@@ -15,6 +15,8 @@ import { type Config } from '../config/config.js';
 import { DEFAULT_FILE_FILTERING_OPTIONS } from '../config/constants.js';
 import { ToolErrorType } from './tool-error.js';
 import { GLOB_TOOL_NAME } from './tool-names.js';
+import { getErrorMessage } from '../utils/errors.js';
+import { debugLogger } from '../utils/debugLogger.js';
 
 // Subset of 'Path' interface provided by 'glob' that we can implement for testing
 export interface GlobPath {
@@ -238,9 +240,8 @@ class GlobToolInvocation extends BaseToolInvocation<
         returnDisplay: `Found ${fileCount} matching file(s)`,
       };
     } catch (error) {
-      const errorMessage =
-        error instanceof Error ? error.message : String(error);
-      console.error(`GlobLogic execute Error: ${errorMessage}`, error);
+      debugLogger.warn(`GlobLogic execute Error`, error);
+      const errorMessage = getErrorMessage(error);
       const rawError = `Error during glob search operation: ${errorMessage}`;
       return {
         llmContent: rawError,
diff --git a/packages/core/src/tools/grep.ts b/packages/core/src/tools/grep.ts
index e2637accb8..d279d65e49 100644
--- a/packages/core/src/tools/grep.ts
+++ b/packages/core/src/tools/grep.ts
@@ -199,7 +199,7 @@ class GrepToolInvocation extends BaseToolInvocation<
         returnDisplay: `Found ${matchCount} ${matchTerm}`,
       };
     } catch (error) {
-      console.error(`Error during GrepLogic execution: ${error}`);
+      debugLogger.warn(`Error during GrepLogic execution: ${error}`);
       const errorMessage = getErrorMessage(error);
       return {
         llmContent: `Error during grep search operation: ${errorMessage}`,
@@ -552,7 +552,7 @@ class GrepToolInvocation extends BaseToolInvocation<
 
       return allMatches;
     } catch (error: unknown) {
-      console.error(
+      debugLogger.warn(
         `GrepLogic: Error in performGrepSearch (Strategy: ${strategyUsed}): ${getErrorMessage(
           error,
         )}`,
diff --git a/packages/core/src/tools/ls.test.ts b/packages/core/src/tools/ls.test.ts
index 1cda0c9e7e..d6c828c94b 100644
--- a/packages/core/src/tools/ls.test.ts
+++ b/packages/core/src/tools/ls.test.ts
@@ -248,11 +248,6 @@ describe('LSTool', () => {
         return originalStat(p);
       });
 
-      // Spy on console.error to verify it's called
-      const consoleErrorSpy = vi
-        .spyOn(console, 'error')
-        .mockImplementation(() => {});
-
       const invocation = lsTool.build({ path: tempRootDir });
       const result = await invocation.execute(abortSignal);
 
@@ -261,13 +256,7 @@ describe('LSTool', () => {
       expect(result.llmContent).not.toContain('problematic.txt');
       expect(result.returnDisplay).toBe('Listed 1 item(s).');
 
-      // Verify error was logged
-      expect(consoleErrorSpy).toHaveBeenCalledWith(
-        expect.stringMatching(/Error accessing.*problematic\.txt/s),
-      );
-
       statSpy.mockRestore();
-      consoleErrorSpy.mockRestore();
     });
   });
 
diff --git a/packages/core/src/tools/ls.ts b/packages/core/src/tools/ls.ts
index 7aac367e50..b899ae8fcc 100644
--- a/packages/core/src/tools/ls.ts
+++ b/packages/core/src/tools/ls.ts
@@ -14,6 +14,7 @@ import type { Config } from '../config/config.js';
 import { DEFAULT_FILE_FILTERING_OPTIONS } from '../config/constants.js';
 import { ToolErrorType } from './tool-error.js';
 import { LS_TOOL_NAME } from './tool-names.js';
+import { debugLogger } from '../utils/debugLogger.js';
 
 /**
  * Parameters for the LS tool
@@ -205,7 +206,7 @@ class LSToolInvocation extends BaseToolInvocation<LSToolParams, ToolResult> {
           });
         } catch (error) {
           // Log error internally but don't fail the whole listing
-          console.error(`Error accessing ${fullPath}: ${error}`);
+          debugLogger.debug(`Error accessing ${fullPath}: ${error}`);
         }
       }