diff --git a/erpnext/accounts/doctype/bank_transaction/bank_transaction.js b/erpnext/accounts/doctype/bank_transaction/bank_transaction.js
index cf041cd3c77..de960533ec4 100644
--- a/erpnext/accounts/doctype/bank_transaction/bank_transaction.js
+++ b/erpnext/accounts/doctype/bank_transaction/bank_transaction.js
@@ -2,7 +2,7 @@
 // For license information, please see license.txt
 
 frappe.ui.form.on('Bank Transaction', {
-	onload: function(frm) {
+	onload(frm) {
 		frm.set_query('payment_document', 'payment_entries', function() {
 			return {
 				"filters": {
@@ -12,3 +12,21 @@ frappe.ui.form.on('Bank Transaction', {
 		});
 	}
 });
+
+frappe.ui.form.on('Bank Transaction Payments', {
+	payment_entries_remove: function(frm, cdt, cdn) {
+		update_clearance_date(frm, cdt, cdn);
+	}
+});
+
+const update_clearance_date = (frm, cdt, cdn) => {
+	if (frm.doc.docstatus === 1) {
+		frappe.xcall('erpnext.accounts.doctype.bank_transaction.bank_transaction.unclear_reference_payment',
+			{doctype: cdt, docname: cdn})
+		.then(e => {
+			if (e == "success") {
+				frappe.show_alert({message:__("Document {0} successfully uncleared", [e]), indicator:'green'});
+			}
+		})
+	}
+}
\ No newline at end of file
diff --git a/erpnext/accounts/doctype/bank_transaction/bank_transaction.json b/erpnext/accounts/doctype/bank_transaction/bank_transaction.json
index e7f6c2c3f3a..b9cef288fb3 100644
--- a/erpnext/accounts/doctype/bank_transaction/bank_transaction.json
+++ b/erpnext/accounts/doctype/bank_transaction/bank_transaction.json
@@ -1,800 +1,833 @@
 {
- "allow_copy": 0, 
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- "allow_guest_to_view": 0, 
- "allow_import": 1, 
- "allow_rename": 0, 
- "autoname": "naming_series:", 
- "beta": 0, 
- "creation": "2018-10-22 18:19:02.784533", 
- "custom": 0, 
- "docstatus": 0, 
- "doctype": "DocType", 
- "document_type": "", 
- "editable_grid": 1, 
- "engine": "InnoDB", 
+ "allow_copy": 0,
+ "allow_events_in_timeline": 0,
+ "allow_guest_to_view": 0,
+ "allow_import": 1,
+ "allow_rename": 0,
+ "autoname": "naming_series:",
+ "beta": 0,
+ "creation": "2018-10-22 18:19:02.784533",
+ "custom": 0,
+ "docstatus": 0,
+ "doctype": "DocType",
+ "document_type": "",
+ "editable_grid": 1,
+ "engine": "InnoDB",
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+   "print_hide_if_no_value": 0,
+   "read_only": 0,
+   "remember_last_selected_value": 0,
+   "report_hide": 0,
+   "reqd": 0,
+   "search_index": 0,
+   "set_only_once": 0,
+   "translatable": 0,
+   "unique": 0
+  },
+  {
+   "allow_bulk_edit": 0,
+   "allow_in_quick_entry": 0,
+   "allow_on_submit": 0,
+   "bold": 0,
+   "collapsible": 0,
+   "columns": 0,
+   "depends_on": "",
+   "fetch_if_empty": 0,
+   "fieldname": "unallocated_amount",
+   "fieldtype": "Currency",
+   "hidden": 0,
+   "ignore_user_permissions": 0,
+   "ignore_xss_filter": 0,
+   "in_filter": 0,
+   "in_global_search": 0,
+   "in_list_view": 0,
+   "in_standard_filter": 0,
+   "label": "Unallocated Amount",
+   "length": 0,
+   "no_copy": 0,
+   "permlevel": 0,
+   "precision": "",
+   "print_hide": 0,
+   "print_hide_if_no_value": 0,
+   "read_only": 0,
+   "remember_last_selected_value": 0,
+   "report_hide": 0,
+   "reqd": 0,
+   "search_index": 0,
+   "set_only_once": 0,
+   "translatable": 0,
    "unique": 0
   }
- ], 
- "has_web_view": 0, 
- "hide_heading": 0, 
- "hide_toolbar": 0, 
- "idx": 0, 
- "image_view": 0, 
- "in_create": 0, 
- "is_submittable": 1, 
- "issingle": 0, 
- "istable": 0, 
- "max_attachments": 0, 
- "modified": "2019-03-22 10:52:04.540756", 
- "modified_by": "Administrator", 
- "module": "Accounts", 
- "name": "Bank Transaction", 
- "name_case": "", 
- "owner": "Administrator", 
+ ],
+ "has_web_view": 0,
+ "hide_heading": 0,
+ "hide_toolbar": 0,
+ "idx": 0,
+ "image_view": 0,
+ "in_create": 0,
+ "is_submittable": 1,
+ "issingle": 0,
+ "istable": 0,
+ "max_attachments": 0,
+ "modified": "2019-04-26 14:32:16.437813",
+ "modified_by": "Administrator",
+ "module": "Accounts",
+ "name": "Bank Transaction",
+ "name_case": "",
+ "owner": "Administrator",
  "permissions": [
   {
-   "amend": 0, 
-   "cancel": 1, 
-   "create": 1, 
-   "delete": 1, 
-   "email": 1, 
-   "export": 1, 
-   "if_owner": 0, 
-   "import": 0, 
-   "permlevel": 0, 
-   "print": 1, 
-   "read": 1, 
-   "report": 1, 
-   "role": "System Manager", 
-   "set_user_permissions": 0, 
-   "share": 1, 
-   "submit": 1, 
+   "amend": 0,
+   "cancel": 1,
+   "create": 1,
+   "delete": 1,
+   "email": 1,
+   "export": 1,
+   "if_owner": 0,
+   "import": 0,
+   "permlevel": 0,
+   "print": 1,
+   "read": 1,
+   "report": 1,
+   "role": "System Manager",
+   "set_user_permissions": 0,
+   "share": 1,
+   "submit": 1,
    "write": 1
-  }, 
+  },
   {
-   "amend": 0, 
-   "cancel": 1, 
-   "create": 1, 
-   "delete": 1, 
-   "email": 1, 
-   "export": 1, 
-   "if_owner": 0, 
-   "import": 0, 
-   "permlevel": 0, 
-   "print": 1, 
-   "read": 1, 
-   "report": 1, 
-   "role": "Accounts Manager", 
-   "set_user_permissions": 0, 
-   "share": 1, 
-   "submit": 1, 
+   "amend": 0,
+   "cancel": 1,
+   "create": 1,
+   "delete": 1,
+   "email": 1,
+   "export": 1,
+   "if_owner": 0,
+   "import": 0,
+   "permlevel": 0,
+   "print": 1,
+   "read": 1,
+   "report": 1,
+   "role": "Accounts Manager",
+   "set_user_permissions": 0,
+   "share": 1,
+   "submit": 1,
    "write": 1
-  }, 
+  },
   {
-   "amend": 0, 
-   "cancel": 0, 
-   "create": 1, 
-   "delete": 1, 
-   "email": 1, 
-   "export": 1, 
-   "if_owner": 0, 
-   "import": 0, 
-   "permlevel": 0, 
-   "print": 1, 
-   "read": 1, 
-   "report": 1, 
-   "role": "Accounts User", 
-   "set_user_permissions": 0, 
-   "share": 1, 
-   "submit": 1, 
+   "amend": 0,
+   "cancel": 0,
+   "create": 1,
+   "delete": 1,
+   "email": 1,
+   "export": 1,
+   "if_owner": 0,
+   "import": 0,
+   "permlevel": 0,
+   "print": 1,
+   "read": 1,
+   "report": 1,
+   "role": "Accounts User",
+   "set_user_permissions": 0,
+   "share": 1,
+   "submit": 1,
    "write": 1
   }
- ], 
- "quick_entry": 0, 
- "read_only": 0, 
- "read_only_onload": 0, 
- "show_name_in_global_search": 0, 
- "sort_field": "date", 
- "sort_order": "DESC", 
- "title_field": "bank_account", 
- "track_changes": 0, 
- "track_seen": 0, 
+ ],
+ "quick_entry": 0,
+ "read_only": 0,
+ "read_only_onload": 0,
+ "show_name_in_global_search": 0,
+ "sort_field": "date",
+ "sort_order": "DESC",
+ "title_field": "bank_account",
+ "track_changes": 0,
+ "track_seen": 0,
  "track_views": 0
 }
\ No newline at end of file
diff --git a/erpnext/accounts/doctype/bank_transaction/bank_transaction.py b/erpnext/accounts/doctype/bank_transaction/bank_transaction.py
index 0050ffc9df2..c923cd2bfee 100644
--- a/erpnext/accounts/doctype/bank_transaction/bank_transaction.py
+++ b/erpnext/accounts/doctype/bank_transaction/bank_transaction.py
@@ -1,19 +1,32 @@
 # -*- coding: utf-8 -*-
-# Copyright (c) 2018, Frappe Technologies Pvt. Ltd. and contributors
+# Copyright (c) 2019, Frappe Technologies Pvt. Ltd. and contributors
 # For license information, please see license.txt
 
 from __future__ import unicode_literals
 import frappe
-from frappe.model.document import Document
+from erpnext.controllers.status_updater import StatusUpdater
 from frappe.utils import flt
 from six.moves import reduce
+from frappe import _
 
-class BankTransaction(Document):
+class BankTransaction(StatusUpdater):
 	def after_insert(self):
 		self.unallocated_amount = abs(flt(self.credit) - flt(self.debit))
 
+	def on_submit(self):
+		self.clear_linked_payment_entries()
+		self.set_status()
+
 	def on_update_after_submit(self):
-		allocated_amount = reduce(lambda x, y: flt(x) + flt(y), [x.allocated_amount for x in self.payment_entries])
+		self.update_allocations()
+		self.clear_linked_payment_entries()
+		self.set_status(update=True)
+
+	def update_allocations(self):
+		if self.payment_entries:
+			allocated_amount = reduce(lambda x, y: flt(x) + flt(y), [x.allocated_amount for x in self.payment_entries])
+		else:
+			allocated_amount = 0
 
 		if allocated_amount:
 			frappe.db.set_value(self.doctype, self.name, "allocated_amount", flt(allocated_amount))
@@ -23,4 +36,69 @@ class BankTransaction(Document):
 			frappe.db.set_value(self.doctype, self.name, "allocated_amount", 0)
 			frappe.db.set_value(self.doctype, self.name, "unallocated_amount", abs(flt(self.credit) - flt(self.debit)))
 
-		self.reload()
\ No newline at end of file
+		self.reload()
+
+	def clear_linked_payment_entries(self):
+		for payment_entry in self.payment_entries:
+			allocated_amount = self.get_total_allocated_amount(payment_entry)
+			print(allocated_amount)
+			paid_amount = self.get_paid_amount(payment_entry)
+
+			if paid_amount and allocated_amount:
+				if  flt(allocated_amount[0]["allocated_amount"]) > flt(paid_amount):
+					frappe.throw(_("The total allocated amount ({0}) is greated than the paid amount ({1}).".format(flt(allocated_amount[0]["allocated_amount"]), flt(paid_amount))))
+			
+				elif flt(allocated_amount[0]["allocated_amount"]) == flt(paid_amount):
+					if payment_entry.payment_document in ["Payment Entry", "Journal Entry", "Purchase Invoice", "Expense Claim"]:
+						self.clear_simple_entry(payment_entry)
+
+					elif payment_entry.payment_document == "Sales Invoice":
+						self.clear_sales_invoice(payment_entry)
+
+	def get_total_allocated_amount(self, payment_entry):
+		return frappe.db.sql("""
+			SELECT
+				SUM(btp.allocated_amount) as allocated_amount,
+				bt.name
+			FROM
+				`tabBank Transaction Payments` as btp
+			LEFT JOIN
+				`tabBank Transaction` bt ON bt.name=btp.parent
+			WHERE
+				btp.payment_document = %s
+			AND
+				btp.payment_entry = %s
+			AND
+				bt.docstatus = 1""", (payment_entry.payment_document, payment_entry.payment_entry), as_dict=True)
+
+	def get_paid_amount(self, payment_entry):
+		if payment_entry.payment_document in ["Payment Entry", "Sales Invoice", "Purchase Invoice"]:
+			return frappe.db.get_value(payment_entry.payment_document, payment_entry.payment_entry, "paid_amount")
+
+		elif payment_entry.payment_document == "Journal Entry":
+			return frappe.db.get_value(payment_entry.payment_document, payment_entry.payment_entry, "total_credit")
+
+		elif payment_entry.payment_document == "Expense Claim":
+			return frappe.db.get_value(payment_entry.payment_document, payment_entry.payment_entry, "total_amount_reimbursed")
+
+		else:
+			frappe.throw("Please reconcile {0}: {1} manually".format(payment_entry.payment_document, payment_entry.payment_entry))
+
+	def clear_simple_entry(self, payment_entry):
+		frappe.db.set_value(payment_entry.payment_document, payment_entry.payment_entry, "clearance_date", self.date)
+
+	def clear_sales_invoice(self, payment_entry):
+		frappe.db.set_value("Sales Invoice Payment", dict(parenttype=payment_entry.payment_document,
+			parent=payment_entry.payment_entry), "clearance_date", self.date)
+
+@frappe.whitelist()
+def unclear_reference_payment(doctype, docname):
+	if frappe.db.exists(doctype, docname):
+		doc = frappe.get_doc(doctype, docname)
+		if doctype == "Sales Invoice":
+			frappe.db.set_value("Sales Invoice Payment", dict(parenttype=doc.payment_document,
+				parent=doc.payment_entry), "clearance_date", None)
+		else:
+			frappe.db.set_value(doc.payment_document, doc.payment_entry, "clearance_date", None)
+
+		return doc.payment_entry
diff --git a/erpnext/accounts/doctype/bank_transaction/bank_transaction_list.js b/erpnext/accounts/doctype/bank_transaction/bank_transaction_list.js
index 44dfaf18766..2ecc2b0cda3 100644
--- a/erpnext/accounts/doctype/bank_transaction/bank_transaction_list.js
+++ b/erpnext/accounts/doctype/bank_transaction/bank_transaction_list.js
@@ -6,7 +6,7 @@ frappe.listview_settings['Bank Transaction'] = {
 	get_indicator: function(doc) {
 		if(flt(doc.unallocated_amount)>0) {
 			return [__("Unreconciled"), "orange", "unallocated_amount,>,0"];
-		} else if(flt(doc.unallocated_amount)===0) {
+		} else if(flt(doc.unallocated_amount)<=0) {
 			return [__("Reconciled"), "green", "unallocated_amount,=,0"];
 		}
 	}
diff --git a/erpnext/accounts/doctype/bank_transaction/bank_transaction_upload.py b/erpnext/accounts/doctype/bank_transaction/bank_transaction_upload.py
index ccee269bced..deedafdfb5d 100644
--- a/erpnext/accounts/doctype/bank_transaction/bank_transaction_upload.py
+++ b/erpnext/accounts/doctype/bank_transaction/bank_transaction_upload.py
@@ -36,7 +36,8 @@ def upload_bank_statement():
 def create_bank_entries(columns, data, bank_account):
 	header_map = get_header_mapping(columns, bank_account)
 
-	count = 0
+	success = 0
+	errors = 0
 	for d in json.loads(data):
 		if all(item is None for item in d) is True:
 			continue
@@ -44,7 +45,6 @@ def create_bank_entries(columns, data, bank_account):
 		for key, value in iteritems(header_map):
 			fields.update({key: d[int(value)-1]})
 
-
 		try:
 			bank_transaction = frappe.get_doc({
 				"doctype": "Bank Transaction"
@@ -54,12 +54,12 @@ def create_bank_entries(columns, data, bank_account):
 			bank_transaction.bank_account = bank_account
 			bank_transaction.insert()
 			bank_transaction.submit()
-			count = count + 1
-		except Exception as e:
-			frappe.throw(e)
+			success += 1
+		except Exception:
 			frappe.log_error(frappe.get_traceback())
+			errors += 1
 
-	return count
+	return {"success": success, "errors": errors}
 
 def get_header_mapping(columns, bank_account):
 	mapping = get_bank_mapping(bank_account)
diff --git a/erpnext/accounts/page/bank_reconciliation/bank_reconciliation.js b/erpnext/accounts/page/bank_reconciliation/bank_reconciliation.js
index c64e28fc218..6eafa0d2310 100644
--- a/erpnext/accounts/page/bank_reconciliation/bank_reconciliation.js
+++ b/erpnext/accounts/page/bank_reconciliation/bank_reconciliation.js
@@ -191,7 +191,7 @@ erpnext.accounts.bankTransactionUpload = class bankTransactionUpload {
 		frappe.xcall('erpnext.accounts.doctype.bank_transaction.bank_transaction_upload.create_bank_entries',
 			{columns: this.datatable.datamanager.columns, data: this.datatable.datamanager.data, bank_account: me.parent.bank_account}
 		).then((result) => {
-			let result_title = __("{0} bank transaction(s) created", [result])
+			let result_title = result.errors == 0 ? __("{0} bank transaction(s) created", [result.success]) : __("{0} bank transaction(s) created and {1} errors", [result.success, result.errors])
 			let result_msg = `
 				<div class="flex justify-center align-center text-muted" style="height: 50vh; display: flex;">
 					<h5 class="text-muted">${result_title}</h5>
@@ -199,7 +199,11 @@ erpnext.accounts.bankTransactionUpload = class bankTransactionUpload {
 			me.parent.page.clear_primary_action();
 			me.parent.$main_section.empty();
 			me.parent.$main_section.append(result_msg);
-			frappe.show_alert({message:__("All bank transactions have been created"), indicator:'green'});
+			if (result.errors == 0) {
+				frappe.show_alert({message:__("All bank transactions have been created"), indicator:'green'});
+			} else {
+				frappe.show_alert({message:__("Please check the error log for details about the import errors"), indicator:'red'});
+			}
 		})
 	}
 }
@@ -530,11 +534,13 @@ erpnext.accounts.ReconciliationRow = class ReconciliationRow {
 			.then(doc => {
 				let displayed_docs = []
 				if (dt === "Payment Entry") {
-					doc.currency = doc.payment_type == "Receive" ? doc.paid_to_account_currency : doc.paid_from_account_currency;
-					displayed_docs.push(doc);
+					payment.currency = doc.payment_type == "Receive" ? doc.paid_to_account_currency : doc.paid_from_account_currency;
+					payment.doctype = dt
+					displayed_docs.push(payment);
 				} else if (dt === "Journal Entry") {
 					doc.accounts.forEach(payment => {
 						if (payment.account === me.gl_account) {
+							payment.doctype = dt;
 							payment.posting_date = doc.posting_date;
 							payment.party = doc.pay_to_recd_from;
 							payment.reference_no = doc.cheque_no;
@@ -548,6 +554,7 @@ erpnext.accounts.ReconciliationRow = class ReconciliationRow {
 				} else if (dt === "Sales Invoice") {
 					doc.payments.forEach(payment => {
 						if (payment.clearance_date === null || payment.clearance_date === "") {
+							payment.doctype = dt;
 							payment.posting_date = doc.posting_date;
 							payment.party = doc.customer;
 							payment.reference_no = doc.remarks;
diff --git a/erpnext/accounts/page/bank_reconciliation/bank_reconciliation.py b/erpnext/accounts/page/bank_reconciliation/bank_reconciliation.py
index e2d6b58766b..f79a04adc58 100644
--- a/erpnext/accounts/page/bank_reconciliation/bank_reconciliation.py
+++ b/erpnext/accounts/page/bank_reconciliation/bank_reconciliation.py
@@ -28,7 +28,7 @@ def reconcile(bank_transaction, payment_doctype, payment_name):
 		frappe.throw(_("The selected payment entry should be linked with a creditor bank transaction"))
 
 	add_payment_to_transaction(transaction, payment_entry, gl_entry)
-	clear_payment_entry(transaction, payment_entry, gl_entry)
+	#clear_payment_entry(transaction, payment_entry, gl_entry)
 
 	return 'reconciled'
 
@@ -42,40 +42,6 @@ def add_payment_to_transaction(transaction, payment_entry, gl_entry):
 	})
 	transaction.save()
 
-def clear_payment_entry(transaction, payment_entry, gl_entry):
-	linked_bank_transactions = frappe.db.sql("""
-		SELECT
-			bt.credit, bt.debit
-		FROM
-			`tabBank Transaction Payments` as btp
-		LEFT JOIN
-			`tabBank Transaction` as bt on btp.parent=bt.name
-		WHERE
-			btp.payment_document = %s
-		AND
-			btp.payment_entry = %s
-		AND
-			bt.docstatus = 1
-	""", (payment_entry.doctype, payment_entry.name), as_dict=True)
-
-	amount_cleared = (flt(linked_bank_transactions[0].credit) - flt(linked_bank_transactions[0].debit))
-	amount_to_be_cleared = (flt(gl_entry.debit) - flt(gl_entry.credit))
-
-	if payment_entry.doctype in ("Payment Entry", "Journal Entry", "Purchase Invoice", "Expense Claim"):
-		clear_simple_entry(amount_cleared, amount_to_be_cleared, payment_entry, transaction)
-
-	elif payment_entry.doctype == "Sales Invoice":
-		clear_sales_invoice(amount_cleared, amount_to_be_cleared, payment_entry, transaction)
-
-def clear_simple_entry(amount_cleared, amount_to_be_cleared, payment_entry, transaction):
-	if amount_cleared >= amount_to_be_cleared:
-		frappe.db.set_value(payment_entry.doctype, payment_entry.name, "clearance_date", transaction.date)
-
-def clear_sales_invoice(amount_cleared, amount_to_be_cleared, payment_entry, transaction):
-	if amount_cleared >= amount_to_be_cleared:
-		frappe.db.set_value("Sales Invoice Payment", dict(parenttype=payment_entry.doctype,
-			parent=payment_entry.name), "clearance_date", transaction.date)
-
 @frappe.whitelist()
 def get_linked_payments(bank_transaction):
 	transaction = frappe.get_doc("Bank Transaction", bank_transaction)
@@ -250,7 +216,7 @@ def get_matching_descriptions_data(company, transaction):
 		if key == "Payment Entry":
 			data.extend(frappe.get_all("Payment Entry", filters=[["name", "in", value]], fields=["'Payment Entry' as doctype", "posting_date", "party", "reference_no", "reference_date", "paid_amount", "paid_to_account_currency as currency"]))
 		if key == "Journal Entry":
-			journal_entries = frappe.get_all("Journal Entry", filters=[["name", "in", value]], fields=["name", "'Journal Entry' as doctype", "posting_date", "paid_to_recd_from as party", "cheque_no as reference_no", "cheque_date as reference_date", "total_credit as paid_amount"])
+			journal_entries = frappe.get_all("Journal Entry", filters=[["name", "in", value]], fields=["name", "'Journal Entry' as doctype", "posting_date", "pay_to_recd_from as party", "cheque_no as reference_no", "cheque_date as reference_date", "total_credit as paid_amount"])
 			for journal_entry in journal_entries:
 				journal_entry_accounts = frappe.get_all("Journal Entry Account", filters={"parenttype": journal_entry["doctype"], "parent": journal_entry["name"]}, fields=["account_currency"])
 				journal_entry["currency"] = journal_entry_accounts[0]["account_currency"] if journal_entry_accounts else company_currency
diff --git a/erpnext/controllers/status_updater.py b/erpnext/controllers/status_updater.py
index d86c3f546c3..b7d2bad17ab 100644
--- a/erpnext/controllers/status_updater.py
+++ b/erpnext/controllers/status_updater.py
@@ -95,6 +95,10 @@ status_map = {
 		["Ordered", "eval:self.status != 'Stopped' and self.per_ordered == 100 and self.docstatus == 1 and self.material_request_type == 'Purchase'"],
 		["Transferred", "eval:self.status != 'Stopped' and self.per_ordered == 100 and self.docstatus == 1 and self.material_request_type == 'Material Transfer'"],
 		["Issued", "eval:self.status != 'Stopped' and self.per_ordered == 100 and self.docstatus == 1 and self.material_request_type == 'Material Issue'"]
+	],
+	"Bank Transaction": [
+		["Unreconciled", "eval:self.docstatus == 1 and self.unallocated_amount>0"],
+		["Reconciled", "eval:self.docstatus == 1 and self.unallocated_amount<=0"]
 	]
 }