diff --git a/src/core/output/outputSort.ts b/src/core/output/outputSort.ts
index 1cc9cdb07..42b84eab7 100644
--- a/src/core/output/outputSort.ts
+++ b/src/core/output/outputSort.ts
@@ -5,8 +5,10 @@ import { logger } from '../../shared/logger.js';
 import type { ProcessedFile } from '../file/fileTypes.js';
 import { getFileChangeCount, isGitInstalled } from '../git/gitRepositoryHandle.js';
 
-// Cache for git file change counts to avoid repeated git operations
+// Cache for git file change counts to avoid repeated git operations.
+// Capped to prevent unbounded growth in long-running MCP server processes.
 // Key format: `${cwd}:${maxCommits}`
+const MAX_CACHE_SIZE = 50;
 const fileChangeCountsCache = new Map<string, Record<string, number>>();
 
 // Cache for git availability check per cwd
@@ -48,6 +50,12 @@ const getFileChangeCounts = async (
   // Fetch from git log
   try {
     const fileChangeCounts = await deps.getFileChangeCount(cwd, maxCommits);
+    if (fileChangeCountsCache.size >= MAX_CACHE_SIZE) {
+      const oldestKey = fileChangeCountsCache.keys().next().value;
+      if (oldestKey !== undefined) {
+        fileChangeCountsCache.delete(oldestKey);
+      }
+    }
     fileChangeCountsCache.set(cacheKey, fileChangeCounts);
 
     logger.trace('Git File change counts max commits:', maxCommits);
diff --git a/src/core/treeSitter/languageParser.ts b/src/core/treeSitter/languageParser.ts
index f9cca5b42..cf0878cf8 100644
--- a/src/core/treeSitter/languageParser.ts
+++ b/src/core/treeSitter/languageParser.ts
@@ -107,8 +107,9 @@ export class LanguageParser {
 
   public async dispose(): Promise<void> {
     for (const resources of this.loadedResources.values()) {
+      resources.query.delete();
       resources.parser.delete();
-      logger.debug(`Deleted parser for language: ${resources.lang}`);
+      logger.debug(`Deleted parser and query for language: ${resources.lang}`);
     }
     this.loadedResources.clear();
     this.initialized = false;
diff --git a/src/core/treeSitter/parseFile.ts b/src/core/treeSitter/parseFile.ts
index e5968ecaf..df0e78c9a 100644
--- a/src/core/treeSitter/parseFile.ts
+++ b/src/core/treeSitter/parseFile.ts
@@ -55,14 +55,15 @@ export const parseFile = async (fileContent: string, filePath: string, config: R
   const processedChunks = new Set<string>();
   const capturedChunks: CapturedChunk[] = [];
 
-  try {
-    // Parse the file content into an Abstract Syntax Tree (AST)
-    const tree = parser.parse(fileContent);
-    if (!tree) {
-      logger.debug(`Failed to parse file: ${filePath}`);
-      return undefined;
-    }
+  // The tree allocates native WASM memory that is not managed by the JS garbage
+  // collector, so it must be explicitly freed via tree.delete().
+  const tree = parser.parse(fileContent);
+  if (!tree) {
+    logger.debug(`Failed to parse file: ${filePath}`);
+    return undefined;
+  }
 
+  try {
     // Get the appropriate parse strategy for the language
     const parseStrategy = await languageParser.getStrategyForLang(lang);
 
@@ -93,6 +94,8 @@ export const parseFile = async (fileContent: string, filePath: string, config: R
     }
   } catch (error: unknown) {
     logger.log(`Error parsing file: ${error}\n`);
+  } finally {
+    tree.delete();
   }
 
   const filteredChunks = filterDuplicatedChunks(capturedChunks);
diff --git a/src/mcp/tools/mcpToolRuntime.ts b/src/mcp/tools/mcpToolRuntime.ts
index bec8138ce..aa9bc29b8 100644
--- a/src/mcp/tools/mcpToolRuntime.ts
+++ b/src/mcp/tools/mcpToolRuntime.ts
@@ -6,11 +6,19 @@ import type { CallToolResult } from '@modelcontextprotocol/sdk/types.js';
 import { generateTreeString } from '../../core/file/fileTreeGenerate.js';
 import type { ProcessedFile } from '../../core/file/fileTypes.js';
 
-// Map to store generated output files
+// Map to store generated output files. Capped to prevent unbounded growth
+// in long-running MCP server processes.
+const MAX_REGISTRY_SIZE = 100;
 const outputFileRegistry = new Map<string, string>();
 
-// Register an output file
+// Register an output file, evicting the oldest entry if at capacity
 export const registerOutputFile = (id: string, filePath: string): void => {
+  if (outputFileRegistry.size >= MAX_REGISTRY_SIZE) {
+    const oldestKey = outputFileRegistry.keys().next().value;
+    if (oldestKey !== undefined) {
+      outputFileRegistry.delete(oldestKey);
+    }
+  }
   outputFileRegistry.set(id, filePath);
 };