diff --git a/workspaces/ballerina/ballerina-extension/src/core/extension.ts b/workspaces/ballerina/ballerina-extension/src/core/extension.ts
index 7565c7ee696..385a28af002 100644
--- a/workspaces/ballerina/ballerina-extension/src/core/extension.ts
+++ b/workspaces/ballerina/ballerina-extension/src/core/extension.ts
@@ -40,6 +40,7 @@ import {
     outputChannel,
     isWindows,
     isWSL,
+    quoteShellPath,
     isSupportedVersion,
     VERSION,
     isSupportedSLVersion,
@@ -1819,7 +1820,8 @@ export class BallerinaExtension {
             debug("[VERSION] Non-Windows platform detected, no extension needed");
         }
 
-        let ballerinaCommand = distPath + 'bal' + exeExtension + ' version';
+        // Build the executable path separately so we can quote it for shell execution
+        let balExecutablePath = distPath + 'bal' + exeExtension;
 
         // Handle WSL environment - prefer native Linux installation over Windows .bat files
         if (isWSL()) {
@@ -1829,26 +1831,28 @@ export class BallerinaExtension {
                     // Check if 'bal' command is available in PATH
                     execSync('which bal', { encoding: 'utf8', timeout: 5000 });
                     // If we get here, 'bal' is available, use it instead of .bat
-                    ballerinaCommand = 'bal version';
+                    balExecutablePath = 'bal';
                     debug("[VERSION] WSL detected native 'bal' command, using it instead of .bat file");
                 } catch (error) {
                     debug("[VERSION] No native 'bal' command found in WSL, will try .bat file");
                     // If the path contains Windows-style paths, we need to handle them properly
-                    if (ballerinaCommand.includes('\\') || ballerinaCommand.match(/^[A-Za-z]:/)) {
+                    if (balExecutablePath.includes('\\') || balExecutablePath.match(/^[A-Za-z]:/)) {
                         debug("[VERSION] WSL detected with Windows path, attempting to convert to WSL path");
                         // Try to convert Windows path to WSL path
-                        const wslPath = ballerinaCommand.replace(/^([A-Za-z]):/, '/mnt/$1').replace(/\\/g, '/').toLowerCase();
-                        debug(`[VERSION] Converted Windows path to WSL path: ${wslPath}`);
-                        ballerinaCommand = wslPath;
+                        balExecutablePath = balExecutablePath.replace(/^([A-Za-z]):/, '/mnt/$1').replace(/\\/g, '/').toLowerCase();
+                        debug(`[VERSION] Converted Windows path to WSL path: ${balExecutablePath}`);
                     }
                 }
             } else {
                 // We have a native Linux installation, use it directly
-                ballerinaCommand = 'bal version';
+                balExecutablePath = 'bal';
                 debug("[VERSION] WSL detected with native Linux installation, using 'bal version'");
             }
         }
 
+        // Quote the executable path to handle spaces in directory names
+        let ballerinaCommand = `${quoteShellPath(balExecutablePath)} version`;
+
         debug(`[VERSION] Executing command: '${ballerinaCommand}'`);
 
         let ballerinaExecutor = '';
diff --git a/workspaces/ballerina/ballerina-extension/src/features/ai/agent/tools/test-runner.ts b/workspaces/ballerina/ballerina-extension/src/features/ai/agent/tools/test-runner.ts
index b92930a7272..4c9774c9834 100644
--- a/workspaces/ballerina/ballerina-extension/src/features/ai/agent/tools/test-runner.ts
+++ b/workspaces/ballerina/ballerina-extension/src/features/ai/agent/tools/test-runner.ts
@@ -19,6 +19,7 @@ import { z } from 'zod';
 import child_process from 'child_process';
 import { CopilotEventHandler } from '../../utils/events';
 import { extension } from '../../../../BalExtensionContext';
+import { quoteShellPath } from '../../../../utils/config';
 import { DIAGNOSTICS_TOOL_NAME } from './diagnostics';
 
 export const TEST_RUNNER_TOOL_NAME = "runTests";
@@ -99,7 +100,7 @@ function parseTestSummary(output: string): string {
 async function runBallerinaTests(cwd: string): Promise<TestRunResult> {
     return new Promise((resolve) => {
         const balCmd = extension.ballerinaExtInstance.getBallerinaCmd();
-        const command = `${balCmd} test`;
+        const command = `${quoteShellPath(balCmd)} test`;
 
         console.log(`[TestRunner] Running: ${command} in ${cwd}`);
 
diff --git a/workspaces/ballerina/ballerina-extension/src/features/debugger/config-provider.ts b/workspaces/ballerina/ballerina-extension/src/features/debugger/config-provider.ts
index fbe1b8472e6..03941c2a0d3 100644
--- a/workspaces/ballerina/ballerina-extension/src/features/debugger/config-provider.ts
+++ b/workspaces/ballerina/ballerina-extension/src/features/debugger/config-provider.ts
@@ -48,6 +48,7 @@ import {
     createVersionNumber
 } from "../../utils";
 import { getProjectWorkingDirectory } from "../../utils/file-utils";
+import { quoteShellPath } from "../../utils/config";
 import { decimal, ExecutableOptions } from 'vscode-languageclient/node';
 import { BAL_NOTEBOOK, getTempFile, NOTEBOOK_CELL_SCHEME } from '../../views/notebook';
 import fileUriToPath from 'file-uri-to-path';
@@ -603,7 +604,8 @@ class BallerinaDebugAdapterDescriptorFactory implements DebugAdapterDescriptorFa
     }
     getScriptPath(args: string[]): string {
         args.push('start-debugger-adapter');
-        return extension.ballerinaExtInstance.getBallerinaCmd();
+        // Quote the path to handle spaces in directory names (used with shell: true)
+        return quoteShellPath(extension.ballerinaExtInstance.getBallerinaCmd());
     }
     getCurrentWorkingDir(): string {
         return path.join(extension.ballerinaExtInstance.ballerinaHome, "bin");
@@ -662,7 +664,7 @@ class BIRunAdapter extends LoggingDebugSession {
                 task: 'run'
             };
 
-            let runCommand: string = `${extension.ballerinaExtInstance.getBallerinaCmd()} run`;
+            let runCommand: string = `${quoteShellPath(extension.ballerinaExtInstance.getBallerinaCmd())} run`;
 
             const programArgs = (args as any).programArgs;
             if (programArgs && programArgs.length > 0) {
diff --git a/workspaces/ballerina/ballerina-extension/src/features/project/cmds/cmd-runner.ts b/workspaces/ballerina/ballerina-extension/src/features/project/cmds/cmd-runner.ts
index ec8018823d2..52383dae9fe 100644
--- a/workspaces/ballerina/ballerina-extension/src/features/project/cmds/cmd-runner.ts
+++ b/workspaces/ballerina/ballerina-extension/src/features/project/cmds/cmd-runner.ts
@@ -18,7 +18,7 @@
 
 import { BallerinaProject } from "@wso2/ballerina-core";
 import { Terminal, window, workspace } from "vscode";
-import { isSupportedSLVersion, isWindows, createVersionNumber } from "../../../utils";
+import { isSupportedSLVersion, isWindows, createVersionNumber, quoteShellPath } from "../../../utils";
 import { extension } from "../../../BalExtensionContext";
 import { TracerMachine } from "../../../features/tracing";
 
@@ -128,7 +128,7 @@ export function runCommandWithConf(file: BallerinaProject | string, executor: st
     }
     let commandText;
     if (cmd === BALLERINA_COMMANDS.OTHER) {
-        commandText = `${executor} ${argsList}`;
+        commandText = `${quoteShellPath(executor)} ${argsList}`;
         terminal = window.createTerminal({ name: TERMINAL_NAME });
     } else {
         let env = {};
@@ -164,7 +164,7 @@ export function runCommandWithConf(file: BallerinaProject | string, executor: st
             }
         }
 
-        commandText = `${executor} ${cmd} ${argsList}`;
+        commandText = `${quoteShellPath(executor)} ${cmd} ${argsList}`;
         if (confPath !== '') {
             const configs = env['BAL_CONFIG_FILES'] ? `${env['BAL_CONFIG_FILES']}:${confPath}` : confPath;
             Object.assign(env, { BAL_CONFIG_FILES: configs });
diff --git a/workspaces/ballerina/ballerina-extension/src/features/testing/runner.ts b/workspaces/ballerina/ballerina-extension/src/features/testing/runner.ts
index b136c9560ae..877f05992d2 100644
--- a/workspaces/ballerina/ballerina-extension/src/features/testing/runner.ts
+++ b/workspaces/ballerina/ballerina-extension/src/features/testing/runner.ts
@@ -34,6 +34,7 @@ import { BALLERINA_COMMANDS } from "../project";
 import { discoverTests, gatherTestItems } from "./discover";
 import { testController, projectRoot } from "./activator";
 import { extension } from "../../BalExtensionContext";
+import { quoteShellPath } from "../../utils/config";
 
 enum EXEC_ARG {
     TESTS = '--tests',
@@ -72,7 +73,7 @@ export function runHandler(request: TestRunRequest, cancellation: CancellationTo
             try {
                 // execute test
                 const executor = extension.ballerinaExtInstance.getBallerinaCmd();
-                const commandText = `${executor} ${BALLERINA_COMMANDS.TEST} ${EXEC_ARG.TESTS} ${testNames} ${EXEC_ARG.COVERAGE}`;
+                const commandText = `${quoteShellPath(executor)} ${BALLERINA_COMMANDS.TEST} ${EXEC_ARG.TESTS} ${testNames} ${EXEC_ARG.COVERAGE}`;
                 await runCommand(commandText, projectRoot);
 
             } catch {
diff --git a/workspaces/ballerina/ballerina-extension/src/utils/config.ts b/workspaces/ballerina/ballerina-extension/src/utils/config.ts
index de73c71053e..c802db2727d 100644
--- a/workspaces/ballerina/ballerina-extension/src/utils/config.ts
+++ b/workspaces/ballerina/ballerina-extension/src/utils/config.ts
@@ -73,6 +73,27 @@ export function isWSL(): boolean {
     );
 }
 
+/**
+ * Wraps a file path in double quotes if it contains spaces,
+ * so it can be safely used in shell command strings.
+ * Handles already-quoted paths and escapes embedded double quotes.
+ */
+export function quoteShellPath(filePath: string): string {
+    // Strip existing surrounding quotes to normalize
+    let normalized = filePath;
+    if (normalized.length >= 2 && normalized.startsWith('"') && normalized.endsWith('"')) {
+        normalized = normalized.slice(1, -1);
+    }
+
+    if (!normalized.includes(' ')) {
+        return normalized;
+    }
+
+    // Escape any embedded double quotes
+    const escaped = normalized.replace(/"/g, '\\"');
+    return `"${escaped}"`;
+}
+
 export function isSupportedVersion(ballerinaExtInstance: BallerinaExtension, supportedRelease: VERSION,
     supportedVersion: number): boolean {
     const ballerinaVersion: string = ballerinaExtInstance.ballerinaVersion.toLocaleLowerCase();
diff --git a/workspaces/ballerina/ballerina-extension/src/utils/migrate-integration.ts b/workspaces/ballerina/ballerina-extension/src/utils/migrate-integration.ts
index 02da6e72759..317fcb0f163 100644
--- a/workspaces/ballerina/ballerina-extension/src/utils/migrate-integration.ts
+++ b/workspaces/ballerina/ballerina-extension/src/utils/migrate-integration.ts
@@ -22,6 +22,7 @@ import { extension } from "../BalExtensionContext";
 import { RPCLayer } from "../RPCLayer";
 import { VisualizerWebview } from "../views/visualizer/webview";
 import { debug } from "./logger";
+import { quoteShellPath } from "./config";
 
 const PROGRESS_COMPLETE = 100;
 
@@ -53,7 +54,7 @@ export async function pullMigrationTool(migrationToolName: string, version: stri
     }
 
     const ballerinaCmd = extension.ballerinaExtInstance.getBallerinaCmd();
-    const command = `${ballerinaCmd} tool pull ${migrationToolName}:${version}`;
+    const command = `${quoteShellPath(ballerinaCmd)} tool pull ${migrationToolName}:${version}`;
     debug(`Executing migration tool pull command: ${command}`);
 
     // 2. This function now returns a promise that wraps the exec lifecycle