diff --git a/erpnext/payroll/doctype/payroll_entry/payroll_entry.js b/erpnext/payroll/doctype/payroll_entry/payroll_entry.js
index 395e56f..94f3f30 100644
--- a/erpnext/payroll/doctype/payroll_entry/payroll_entry.js
+++ b/erpnext/payroll/doctype/payroll_entry/payroll_entry.js
@@ -138,7 +138,6 @@
 	payroll_frequency: function (frm) {
 		frm.trigger("set_start_end_dates").then( ()=> {
 			frm.events.clear_employee_table(frm);
-			frm.events.get_employee_with_salary_slip_and_set_query(frm);
 		});
 	},
 
@@ -146,13 +145,17 @@
 		frm.set_query('employee', 'employees', () => {
 			return {
 				filters: {
-					name: ["not in", emp_list]
+					name: ["not in", emp_list],
+					company: frm.doc.company
 				}
 			};
 		});
 	},
 
 	get_employee_with_salary_slip_and_set_query: function (frm) {
+		if (!frm.doc.company) {
+			frappe.throw(__("Please set a Company"));
+		}
 		frappe.db.get_list('Salary Slip', {
 			filters: {
 				start_date: frm.doc.start_date,
@@ -171,6 +174,7 @@
 
 	company: function (frm) {
 		frm.events.clear_employee_table(frm);
+		frm.events.get_employee_with_salary_slip_and_set_query(frm);
 		erpnext.accounts.dimensions.update_dimension(frm, frm.doctype);
 	},
 
@@ -348,6 +352,9 @@
 
 frappe.ui.form.on('Payroll Employee Detail', {
 	employee: function(frm) {
+		if (!frm.doc.company) {
+			frappe.throw(__("Please set a Company"));
+		}
 		if (!frm.doc.payroll_frequency) {
 			frappe.throw(__("Please set a Payroll Frequency"));
 		}
diff --git a/erpnext/payroll/doctype/payroll_entry/payroll_entry.py b/erpnext/payroll/doctype/payroll_entry/payroll_entry.py
index 6bcd4e0..1ed3332 100644
--- a/erpnext/payroll/doctype/payroll_entry/payroll_entry.py
+++ b/erpnext/payroll/doctype/payroll_entry/payroll_entry.py
@@ -14,7 +14,7 @@
 class PayrollEntry(Document):
 	def onload(self):
 		if not self.docstatus==1 or self.salary_slips_submitted:
-    			return
+				return
 
 		# check if salary slips were manually submitted
 		entries = frappe.db.count("Salary Slip", {'payroll_entry': self.name, 'docstatus': 1}, ['name'])
@@ -174,13 +174,12 @@
 		"""
 			Returns list of salary slips based on selected criteria
 		"""
-		cond = self.get_filter_condition()
 
 		ss_list = frappe.db.sql("""
 			select t1.name, t1.salary_structure, t1.payroll_cost_center from `tabSalary Slip` t1
-			where t1.docstatus = %s and t1.start_date >= %s and t1.end_date <= %s
-			and (t1.journal_entry is null or t1.journal_entry = "") and ifnull(salary_slip_based_on_timesheet,0) = %s %s
-		""" % ('%s', '%s', '%s','%s', cond), (ss_status, self.start_date, self.end_date, self.salary_slip_based_on_timesheet), as_dict=as_dict)
+			where t1.docstatus = %s and t1.start_date >= %s and t1.end_date <= %s and t1.payroll_entry = %s
+			and (t1.journal_entry is null or t1.journal_entry = "") and ifnull(salary_slip_based_on_timesheet,0) = %s
+		""", (ss_status, self.start_date, self.end_date, self.name, self.salary_slip_based_on_timesheet), as_dict=as_dict)
 		return ss_list
 
 	def submit_salary_slips(self):
@@ -332,10 +331,9 @@
 	def make_payment_entry(self):
 		self.check_permission('write')
 
-		cond = self.get_filter_condition()
 		salary_slip_name_list = frappe.db.sql(""" select t1.name from `tabSalary Slip` t1
-			where t1.docstatus = 1 and start_date >= %s and end_date <= %s %s
-			""" % ('%s', '%s', cond), (self.start_date, self.end_date), as_list = True)
+			where t1.docstatus = 1 and start_date >= %s and end_date <= %s and t1.payroll_entry = %s
+			""", (self.start_date, self.end_date, self.name), as_list = True)
 
 		if salary_slip_name_list and len(salary_slip_name_list) > 0:
 			salary_slip_total = 0
@@ -550,6 +548,7 @@
 def create_salary_slips_for_employees(employees, args, publish_progress=True):
 	salary_slips_exists_for = get_existing_salary_slips(employees, args)
 	count=0
+	salary_slips_not_created = []
 	for emp in employees:
 		if emp not in salary_slips_exists_for:
 			args.update({
@@ -562,26 +561,18 @@
 			if publish_progress:
 				frappe.publish_progress(count*100/len(set(employees) - set(salary_slips_exists_for)),
 					title = _("Creating Salary Slips..."))
-		else:
-			salary_slip_name = frappe.db.sql(
-				'''SELECT
-						name
-					FROM `tabSalary Slip`
-					WHERE company=%s
-					AND start_date >= %s
-					AND end_date <= %s
-					AND employee = %s
-				''', (args.company, args.start_date, args.end_date, emp), as_dict=True)
 
-			salary_slip_doc = frappe.get_doc('Salary Slip', salary_slip_name[0].name)
-			salary_slip_doc.exchange_rate = args.exchange_rate
-			salary_slip_doc.set_totals()
-			salary_slip_doc.db_update()
+		else:
+			salary_slips_not_created.append(emp)
 
 	payroll_entry = frappe.get_doc("Payroll Entry", args.payroll_entry)
 	payroll_entry.db_set("salary_slips_created", 1)
 	payroll_entry.notify_update()
 
+	if salary_slips_not_created:
+		frappe.msgprint(_("Salary Slips already exists for employees {}, and will not be processed by this payroll.")
+			.format(frappe.bold(", ".join([emp for emp in salary_slips_not_created]))) , title=_("Message"), indicator="orange")
+
 def get_existing_salary_slips(employees, args):
 	return frappe.db.sql_list("""
 		select distinct employee from `tabSalary Slip`