diff --git a/frappe/core/doctype/report/report.py b/frappe/core/doctype/report/report.py
index 2d49915f59..967b28b8b2 100644
--- a/frappe/core/doctype/report/report.py
+++ b/frappe/core/doctype/report/report.py
@@ -6,7 +6,7 @@ import frappe
 import json, datetime
 from frappe import _, scrub
 import frappe.desk.query_report
-from frappe.utils import cint
+from frappe.utils import cint, cstr
 from frappe.model.document import Document
 from frappe.modules.export_file import export_to_files
 from frappe.modules import make_boilerplate
@@ -92,6 +92,18 @@ class Report(Document):
 			make_boilerplate("controller.py", self, {"name": self.name})
 			make_boilerplate("controller.js", self, {"name": self.name})
 
+	def execute_query_report(self, filters):
+		if not self.query:
+			frappe.throw(_("Must specify a Query to run"), title=_('Report Document Error'))
+
+		if not self.query.lower().startswith("select"):
+			frappe.throw(_("Query must be a SELECT"), title=_('Report Document Error'))
+
+		result = [list(t) for t in frappe.db.sql(self.query, filters)]
+		columns = [cstr(c[0]) for c in frappe.db.get_description()]
+
+		return [columns, result]
+
 	def execute_script_report(self, filters):
 		# save the timestamp to automatically set to prepared
 		threshold = 30
diff --git a/frappe/core/utils.py b/frappe/core/utils.py
index 55767ffe34..55cfbc34d7 100644
--- a/frappe/core/utils.py
+++ b/frappe/core/utils.py
@@ -67,3 +67,19 @@ def find_all(list_of_dict, match_function):
 		if match_function(entry):
 			found.append(entry)
 	return found
+
+def ljust_list(_list, length, fill_word=None):
+	"""
+	Similar to ljust but for list.
+
+	Usage:
+		$ ljust_list([1, 2, 3], 5)
+		> [1, 2, 3, None, None]
+	"""
+	# make a copy to avoid mutation of passed list
+	_list = list(_list)
+	fill_length = length - len(_list)
+	if fill_length > 0:
+		_list.extend([fill_word] * fill_length)
+
+	return _list
diff --git a/frappe/desk/query_report.py b/frappe/desk/query_report.py
index d210af02fd..aaf859e7fd 100644
--- a/frappe/desk/query_report.py
+++ b/frappe/desk/query_report.py
@@ -8,7 +8,7 @@ import os, json
 
 from frappe import _
 from frappe.modules import scrub, get_module_path
-from frappe.utils import flt, cint, get_html_format, cstr, get_url_to_form
+from frappe.utils import flt, cint, get_html_format, get_url_to_form
 from frappe.model.utils import render_include
 from frappe.translate import send_translations
 import frappe.desk.reportview
@@ -16,6 +16,7 @@ from frappe.permissions import get_role_permissions
 from six import string_types, iteritems
 from datetime import timedelta
 from frappe.utils import gzip_decompress
+from frappe.core.utils import ljust_list
 
 def get_report_doc(report_name):
 	doc = frappe.get_doc("Report", report_name)
@@ -42,44 +43,32 @@ def get_report_doc(report_name):
 	return doc
 
 
-def generate_report_result(report, filters=None, user=None):
-	status = None
-	if not user:
-		user = frappe.session.user
-	if not filters:
-		filters = []
+def generate_report_result(report, filters=None, user=None, custom_columns=None):
+	user = user or frappe.session.user
+	filters = filters or []
 
 	if filters and isinstance(filters, string_types):
 		filters = json.loads(filters)
-	columns, result, message, chart, report_summary, skip_total_row = [], [], None, None, None, 0
+
+	res = []
+
 	if report.report_type == "Query Report":
-		if not report.query:
-			status = "error"
-			frappe.msgprint(_("Must specify a Query to run"), raise_exception=True)
-
-		if not report.query.lower().startswith("select"):
-			status = "error"
-			frappe.msgprint(_("Query must be a SELECT"), raise_exception=True)
-
-		result = [list(t) for t in frappe.db.sql(report.query, filters)]
-		columns = [cstr(c[0]) for c in frappe.db.get_description()]
+		res = report.execute_query_report(filters)
 
 	elif report.report_type == 'Script Report':
 		res = report.execute_script_report(filters)
 
-		columns, result = res[0], res[1]
-		if len(res) > 2:
-			message = res[2]
-		if len(res) > 3:
-			chart = res[3]
-		if len(res) > 4:
-			report_summary = res[4]
-		if len(res) > 5:
-			skip_total_row = cint(res[5])
+	columns, result, message, chart, report_summary, skip_total_row = \
+		ljust_list(res, 6)
 
 	if report.custom_columns:
 		columns = json.loads(report.custom_columns)
 		result = add_data_to_custom_columns(columns, result)
+	if custom_columns:
+		result = add_data_to_custom_columns(custom_columns, result)
+
+		for custom_column in custom_columns:
+			columns.insert(custom_column['insert_after_index'] + 1, custom_column)
 
 	if result:
 		result = get_filtered_data(report.ref_doctype, columns, result, user)
@@ -93,8 +82,8 @@ def generate_report_result(report, filters=None, user=None):
 		"message": message,
 		"chart": chart,
 		"report_summary": report_summary,
-		"skip_total_row": skip_total_row,
-		"status": status,
+		"skip_total_row": skip_total_row or 0,
+		"status": None,
 		"execution_time": frappe.cache().hget('report_execution_time', report.name) or 0
 	}
 
@@ -161,7 +150,7 @@ def get_script(report_name):
 
 @frappe.whitelist()
 @frappe.read_only()
-def run(report_name, filters=None, user=None, ignore_prepared_report=False):
+def run(report_name, filters=None, user=None, ignore_prepared_report=False, custom_columns=None):
 
 	report = get_report_doc(report_name)
 	if not user:
@@ -183,7 +172,7 @@ def run(report_name, filters=None, user=None, ignore_prepared_report=False):
 			dn = ""
 		result = get_prepared_report_result(report, filters, dn, user)
 	else:
-		result = generate_report_result(report, filters, user)
+		result = generate_report_result(report, filters, user, custom_columns)
 
 	result["add_total_row"] = report.add_total_row and not result.get('skip_total_row', False)
 
@@ -294,6 +283,8 @@ def export_query():
 	if isinstance(data.get("file_format_type"), string_types):
 		file_format_type = data["file_format_type"]
 
+	custom_columns = frappe.parse_json(data["custom_columns"])
+
 	include_indentation = data["include_indentation"]
 	if isinstance(data.get("visible_idx"), string_types):
 		visible_idx = json.loads(data.get("visible_idx"))
@@ -301,7 +292,7 @@ def export_query():
 		visible_idx = None
 
 	if file_format_type == "Excel":
-		data = run(report_name, filters)
+		data = run(report_name, filters, custom_columns=custom_columns)
 		data = frappe._dict(data)
 		if not data.columns:
 			frappe.respond_as_web_page(_("No data to export"),
diff --git a/frappe/public/js/frappe/views/reports/query_report.js b/frappe/public/js/frappe/views/reports/query_report.js
index 1d7065e70d..2276bc07d6 100644
--- a/frappe/public/js/frappe/views/reports/query_report.js
+++ b/frappe/public/js/frappe/views/reports/query_report.js
@@ -616,6 +616,7 @@ frappe.views.QueryReport = class QueryReport extends frappe.views.BaseList {
 	prepare_report_data(data) {
 		this.raw_data = data;
 		this.columns = this.prepare_columns(data.columns);
+		this.custom_columns = [];
 		this.data = this.prepare_data(data.result);
 		this.linked_doctypes = this.get_linked_doctypes();
 		this.tree_report = this.data.some(d => 'indent' in d);
@@ -1110,6 +1111,7 @@ frappe.views.QueryReport = class QueryReport extends frappe.views.BaseList {
 				const args = {
 					cmd: 'frappe.desk.query_report.export_query',
 					report_name: this.report_name,
+					custom_columns: this.custom_columns.length? this.custom_columns: [],
 					file_format_type: file_format,
 					filters: filters,
 					visible_idx,
@@ -1275,16 +1277,20 @@ frappe.views.QueryReport = class QueryReport extends frappe.views.BaseList {
 						primary_action: (values) => {
 							const custom_columns = [];
 							let df = frappe.meta.get_docfield(values.doctype, values.field);
+							const insert_after_index = this.columns
+								.findIndex(column => column.label === values.insert_after);
 							custom_columns.push({
 								fieldname: df.fieldname,
 								fieldtype: df.fieldtype,
 								label: df.label,
+								insert_after_index: insert_after_index,
 								link_field: this.doctype_field_map[values.doctype],
 								doctype: values.doctype,
 								options: df.fieldtype === "Link" ? df.options : undefined,
 								width: 100
 							});
 
+							this.custom_columns = this.custom_columns.concat(custom_columns);
 							frappe.call({
 								method: 'frappe.desk.query_report.get_data_for_custom_field',
 								args: {
@@ -1294,7 +1300,8 @@ frappe.views.QueryReport = class QueryReport extends frappe.views.BaseList {
 								callback: (r) => {
 									const custom_data = r.message;
 									const link_field = this.doctype_field_map[values.doctype];
-									this.add_custom_column(custom_columns, custom_data, link_field, values.field, values.insert_after);
+
+									this.add_custom_column(custom_columns, custom_data, link_field, values.field, insert_after_index);
 									d.hide();
 								}
 							});
@@ -1369,11 +1376,9 @@ frappe.views.QueryReport = class QueryReport extends frappe.views.BaseList {
 		}
 	}
 
-	add_custom_column(custom_column, custom_data, link_field, column_field, insert_after) {
+	add_custom_column(custom_column, custom_data, link_field, column_field, insert_after_index) {
 		const column = this.prepare_columns(custom_column);
 
-		const insert_after_index = this.columns
-			.findIndex(column => column.label === insert_after);
 		this.columns.splice(insert_after_index + 1, 0, column[0]);
 
 		this.data.forEach(row => {