diff --git a/pyproject.toml b/pyproject.toml
index f02b5559..59adf952 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -88,6 +88,7 @@ dependencies = [
     "anthropic == 0.26.1",
     "docx2txt == 0.8",
     "google-generativeai == 0.8.3",
+    "pyjson5 == 1.6.7",
 ]
 dynamic = ["version"]
 
diff --git a/src/khoj/processor/conversation/utils.py b/src/khoj/processor/conversation/utils.py
index 21a95a29..079f3fea 100644
--- a/src/khoj/processor/conversation/utils.py
+++ b/src/khoj/processor/conversation/utils.py
@@ -5,6 +5,7 @@ import math
 import mimetypes
 import os
 import queue
+import re
 import uuid
 from dataclasses import dataclass
 from datetime import datetime
@@ -14,6 +15,7 @@ from time import perf_counter
 from typing import Any, Callable, Dict, List, Optional
 
 import PIL.Image
+import pyjson5
 import requests
 import tiktoken
 import yaml
@@ -538,6 +540,47 @@ def clean_code_python(code: str):
     return code.strip().removeprefix("```python").removesuffix("```")
 
 
+def load_complex_json(json_str):
+    """
+    Preprocess a raw JSON string to escape unescaped double quotes within value strings,
+    while preserving the JSON structure and already escaped quotes.
+    """
+
+    def replace_unescaped_quotes(match):
+        # Get the content between colons and commas/end braces
+        content = match.group(1)
+        # Replace unescaped double, single quotes that aren't already escaped
+        # Uses negative lookbehind to avoid replacing already escaped quotes
+        # Replace " with \"
+        processed_dq = re.sub(r'(?<!\\)"', '\\"', content)
+        # Replace \' with \\'
+        processed_final = re.sub(r"(?<!\\)\\'", r"\\\\'", processed_dq)
+        return f': "{processed_final}"'
+
+    # Match content between : and either , or }
+    # This pattern looks for ': ' followed by any characters until , or }
+    pattern = r':\s*"(.*?)(?<!\\)"(?=[,}])'
+
+    # Process the JSON string
+    cleaned = clean_json(rf"{json_str}")
+    processed = re.sub(pattern, replace_unescaped_quotes, cleaned)
+
+    # See which json loader can load the processed JSON as valid
+    errors = []
+    json_loaders_to_try = [json.loads, pyjson5.loads]
+    for loads in json_loaders_to_try:
+        try:
+            return loads(processed)
+        except (json.JSONDecodeError, pyjson5.Json5Exception) as e:
+            errors.append(f"{type(e).__name__}: {str(e)}")
+
+    # If all loaders fail, raise the aggregated error
+    raise ValueError(
+        f"Failed to load JSON with errors: {'; '.join(errors)}\n\n"
+        f"While attempting to load this cleaned JSON:\n{processed}"
+    )
+
+
 def defilter_query(query: str):
     """Remove any query filters in query"""
     defiltered_query = query
diff --git a/src/khoj/processor/tools/run_code.py b/src/khoj/processor/tools/run_code.py
index 22c8eca5..6c1eb125 100644
--- a/src/khoj/processor/tools/run_code.py
+++ b/src/khoj/processor/tools/run_code.py
@@ -1,6 +1,5 @@
 import base64
 import datetime
-import json
 import logging
 import mimetypes
 import os
@@ -15,8 +14,8 @@ from khoj.processor.conversation import prompts
 from khoj.processor.conversation.utils import (
     ChatEvent,
     clean_code_python,
-    clean_json,
     construct_chat_history,
+    load_complex_json,
 )
 from khoj.routers.helpers import send_message_to_model_wrapper
 from khoj.utils.helpers import is_none_or_empty, timer, truncate_code_context
@@ -135,8 +134,7 @@ async def generate_python_code(
     )
 
     # Validate that the response is a non-empty, JSON-serializable list
-    response = clean_json(response)
-    response = json.loads(response)
+    response = load_complex_json(response)
     code = response.get("code", "").strip()
     input_files = response.get("input_files", [])
     input_links = response.get("input_links", [])
diff --git a/src/khoj/routers/research.py b/src/khoj/routers/research.py
index efeb3787..4417e8fe 100644
--- a/src/khoj/routers/research.py
+++ b/src/khoj/routers/research.py
@@ -1,4 +1,3 @@
-import json
 import logging
 from datetime import datetime
 from typing import Callable, Dict, List, Optional
@@ -10,10 +9,10 @@ from khoj.database.models import Agent, KhojUser
 from khoj.processor.conversation import prompts
 from khoj.processor.conversation.utils import (
     InformationCollectionIteration,
-    clean_json,
     construct_chat_history,
     construct_iteration_history,
     construct_tool_chat_history,
+    load_complex_json,
 )
 from khoj.processor.tools.online_search import read_webpages, search_online
 from khoj.processor.tools.run_code import run_code
@@ -106,8 +105,7 @@ async def apick_next_tool(
         return
 
     try:
-        response = clean_json(response)
-        response = json.loads(response)
+        response = load_complex_json(response)
         selected_tool = response.get("tool", None)
         generated_query = response.get("query", None)
         scratchpad = response.get("scratchpad", None)
diff --git a/tests/test_conversation_utils.py b/tests/test_conversation_utils.py
index 2f7a9862..54fe2a7f 100644
--- a/tests/test_conversation_utils.py
+++ b/tests/test_conversation_utils.py
@@ -104,6 +104,18 @@ class TestTruncateMessage:
         assert truncated_chat_history[0] != copy_big_chat_message
 
 
+def test_load_complex_raw_json_string():
+    # Arrange
+    raw_json = r"""{"key": "value with unescaped " and unescaped \' and escaped \" and escaped \\'"}"""
+    expeced_json = {"key": "value with unescaped \" and unescaped \\' and escaped \" and escaped \\'"}
+
+    # Act
+    parsed_json = utils.load_complex_json(raw_json)
+
+    # Assert
+    assert parsed_json == expeced_json
+
+
 def generate_content(count):
     return " ".join([f"{index}" for index, _ in enumerate(range(count))])