diff --git a/erpnext/accounts/doctype/journal_entry/journal_entry.py b/erpnext/accounts/doctype/journal_entry/journal_entry.py
index fe2ef1c5a91..4de20a17389 100644
--- a/erpnext/accounts/doctype/journal_entry/journal_entry.py
+++ b/erpnext/accounts/doctype/journal_entry/journal_entry.py
@@ -6,7 +6,7 @@ import json
 
 import frappe
 from frappe import _, msgprint, scrub
-from frappe.utils import cstr, flt, fmt_money, formatdate, get_link_to_form, nowdate
+from frappe.utils import comma_and, cstr, flt, fmt_money, formatdate, get_link_to_form, nowdate
 
 import erpnext
 from erpnext.accounts.deferred_revenue import get_deferred_booking_accounts
@@ -146,6 +146,7 @@ class JournalEntry(AccountsController):
 		self.validate_empty_accounts_table()
 		self.validate_inter_company_accounts()
 		self.validate_depr_entry_voucher_type()
+		self.validate_advance_accounts()
 
 		if self.docstatus == 0:
 			self.apply_tax_withholding()
@@ -153,6 +154,20 @@ class JournalEntry(AccountsController):
 		if not self.title:
 			self.title = self.get_title()
 
+	def validate_advance_accounts(self):
+		journal_accounts = set([x.account for x in self.accounts])
+		advance_accounts = set()
+		advance_accounts.add(
+			frappe.get_cached_value("Company", self.company, "default_advance_received_account")
+		)
+		advance_accounts.add(frappe.get_cached_value("Company", self.company, "default_advance_paid_account"))
+		if advance_accounts_used := journal_accounts & advance_accounts:
+			frappe.msgprint(
+				_(
+					"Making Journal Entries against advance accounts: {0} is not recommended. These Journals won't be available for Reconciliation."
+				).format(frappe.bold(comma_and(advance_accounts_used)))
+			)
+
 	def validate_for_repost(self):
 		validate_docs_for_voucher_types(["Journal Entry"])
 		validate_docs_for_deferred_accounting([self.name], [])
diff --git a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.json b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.json
index 666926f00eb..219d6089a57 100644
--- a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.json
+++ b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.json
@@ -195,6 +195,8 @@
   },
   {
    "depends_on": "eval:doc.party",
+   "description": "Only 'Payment Entries' made against this advance account are supported.",
+   "documentation_url": "https://docs.erpnext.com/docs/user/manual/en/advance-in-separate-party-account",
    "fieldname": "default_advance_account",
    "fieldtype": "Link",
    "label": "Default Advance Account",
@@ -229,7 +231,7 @@
  "is_virtual": 1,
  "issingle": 1,
  "links": [],
- "modified": "2023-12-14 13:38:16.264013",
+ "modified": "2024-04-23 12:38:29.557315",
  "modified_by": "Administrator",
  "module": "Accounts",
  "name": "Payment Reconciliation",
diff --git a/erpnext/setup/doctype/company/company.json b/erpnext/setup/doctype/company/company.json
index 24d7da45b84..c222d6b96a7 100644
--- a/erpnext/setup/doctype/company/company.json
+++ b/erpnext/setup/doctype/company/company.json
@@ -707,6 +707,8 @@
   },
   {
    "depends_on": "eval:doc.book_advance_payments_in_separate_party_account",
+   "description": "Only 'Payment Entries' made against this advance account are supported.",
+   "documentation_url": "https://docs.erpnext.com/docs/user/manual/en/advance-in-separate-party-account",
    "fieldname": "default_advance_received_account",
    "fieldtype": "Link",
    "label": "Default Advance Received Account",
@@ -715,6 +717,8 @@
   },
   {
    "depends_on": "eval:doc.book_advance_payments_in_separate_party_account",
+   "description": "Only 'Payment Entries' made against this advance account are supported.",
+   "documentation_url": "https://docs.erpnext.com/docs/user/manual/en/advance-in-separate-party-account",
    "fieldname": "default_advance_paid_account",
    "fieldtype": "Link",
    "label": "Default Advance Paid Account",
@@ -782,7 +786,7 @@
  "image_field": "company_logo",
  "is_tree": 1,
  "links": [],
- "modified": "2023-09-10 21:53:13.860791",
+ "modified": "2024-04-23 12:38:33.173938",
  "modified_by": "Administrator",
  "module": "Setup",
  "name": "Company",
diff --git a/erpnext/setup/doctype/company/company.py b/erpnext/setup/doctype/company/company.py
index 7181e90139e..3523cac822e 100644
--- a/erpnext/setup/doctype/company/company.py
+++ b/erpnext/setup/doctype/company/company.py
@@ -35,7 +35,7 @@ class Company(NestedSet):
 		auto_exchange_rate_revaluation: DF.Check
 		book_advance_payments_in_separate_party_account: DF.Check
 		capital_work_in_progress_account: DF.Link | None
-		chart_of_accounts: DF.Literal
+		chart_of_accounts: DF.Literal[None]
 		company_description: DF.TextEditor | None
 		company_logo: DF.AttachImage | None
 		company_name: DF.Data