diff --git a/CHANGELOG.md b/CHANGELOG.md
index aeab62346..60999075d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@
 1. [#5856](https://github.com/influxdata/chronograf/pull/5856): Add alert rule options to not send alert on state recovery and send regardless of state change.
 1. [#5893](https://github.com/influxdata/chronograf/pull/5893): Make aggregation function selection optional.
 1. [#5894](https://github.com/influxdata/chronograf/pull/5894): Autocomplete builtin `v` object in Flux editor.
+1. [#5895](https://github.com/influxdata/chronograf/pull/5895): Warn before overriding the existing Flux Editor script.
 
 ### Bug Fixes
 
diff --git a/ui/src/shared/components/TimeMachine/FluxQueryMaker.tsx b/ui/src/shared/components/TimeMachine/FluxQueryMaker.tsx
index 37276f946..77ded6d46 100644
--- a/ui/src/shared/components/TimeMachine/FluxQueryMaker.tsx
+++ b/ui/src/shared/components/TimeMachine/FluxQueryMaker.tsx
@@ -172,6 +172,7 @@ class FluxQueryMaker extends PureComponent<Props, State> {
 
     return (
       <FluxQueryBuilder
+        script={draftScript}
         source={source}
         timeRange={timeRange}
         onSubmit={this.handleSubmitBuilderScript}
diff --git a/ui/src/shared/components/TimeMachine/fluxQueryBuilder/FluxQueryBuilder.scss b/ui/src/shared/components/TimeMachine/fluxQueryBuilder/FluxQueryBuilder.scss
index 06304603f..3d6fbd2fa 100644
--- a/ui/src/shared/components/TimeMachine/fluxQueryBuilder/FluxQueryBuilder.scss
+++ b/ui/src/shared/components/TimeMachine/fluxQueryBuilder/FluxQueryBuilder.scss
@@ -185,6 +185,9 @@ $flux-form-control-checkbox-gap: 20px;
     margin-right: 4px;
     &:last-child {
       flex-grow: 1;
+      .fqb--submit {
+        width: 100%;
+      }
     }
   }
 }
@@ -208,3 +211,42 @@ button.flux-query-builder--add-card-button {
   font-size: 13px;
   margin-left: 4px;
 }
+
+.fqb--confirm-popup {
+  position: fixed;
+  align-items: center;
+  width: 350px;
+  user-select: none;
+  padding: 8px;
+  background-color: #202028;
+  border-color: #ff8564;
+  border-style: solid;
+  border-width: 2px;
+  border-radius: 6px;
+  box-shadow: 0 0 5px 0 #dc4e58;
+  font-size: 1.1em;
+  display: flex;
+  z-index: 5000;
+
+  .fqb--confirm-label {
+    margin: 0 8px
+  }
+  > button {
+    color: #fff;
+    background: #bf3d5e;
+    background-image: linear-gradient(45deg, rgb(191, 61, 94) 0%, rgb(249, 95, 83) 100%)
+  }
+}
+.fqb--confirm-caret {
+  content: "";
+  width: 0;
+  height: 0;
+  position: fixed;
+  border-top: 6px solid transparent;
+  border-bottom: 6px solid #ff8564;
+  border-left: 6px solid transparent;
+  border-right: 6px solid transparent;
+  margin-top: -12px;
+  margin-left: -3px;
+  z-index: 9999;
+}
diff --git a/ui/src/shared/components/TimeMachine/fluxQueryBuilder/FluxQueryBuilder.tsx b/ui/src/shared/components/TimeMachine/fluxQueryBuilder/FluxQueryBuilder.tsx
index b30bce078..48bf57a61 100644
--- a/ui/src/shared/components/TimeMachine/fluxQueryBuilder/FluxQueryBuilder.tsx
+++ b/ui/src/shared/components/TimeMachine/fluxQueryBuilder/FluxQueryBuilder.tsx
@@ -9,7 +9,6 @@ import FancyScrollbar from '../../FancyScrollbar'
 import {
   Button,
   ButtonShape,
-  ComponentColor,
   ComponentSize,
   ComponentStatus,
   IconFont,
@@ -18,7 +17,6 @@ import AggregationSelector from './AggregationSelector'
 import TagSelector from './TagSelector'
 import {notify as notifyActionCreator} from 'src/shared/actions/notifications'
 import {
-  fluxWizardError,
   notifyCopyToClipboardFailed,
   notifyCopyToClipboardSuccess,
 } from 'src/shared/copy/notifications'
@@ -28,11 +26,12 @@ import timeRangeWindowPeriod from './util/timeRangeWindowPeriod'
 import {RemoteDataState, TimeZones} from 'src/types'
 import {buildQuery} from './util/generateFlux'
 import {timeRangeLabel} from '../../TimeRangeLabel'
+import FluxQueryBuilderSubmit from './FluxQueryBuilderSubmit'
 
 interface OwnProps extends TimeMachineQueryProps {
   onSubmit: (script: string) => void
   onShowEditor: () => void
-  isRunnable: boolean
+  script: string
 }
 
 type Props = OwnProps & typeof mdtp & ReturnType<typeof mstp>
@@ -48,6 +47,7 @@ const FluxQueryBuilder = ({
   onSubmit,
   onShowEditor,
   onAddTagSelector,
+  script: editorScript,
 }: Props) => {
   const [defaultPeriod, timeRangeText] = useMemo(
     () => [
@@ -97,7 +97,7 @@ const FluxQueryBuilder = ({
             <Button
               shape={ButtonShape.Square}
               size={ComponentSize.ExtraSmall}
-              titleText="Copy builder query to clipboard"
+              titleText="Copy builder script to clipboard"
               icon={IconFont.Duplicate}
               status={
                 isRunnable ? ComponentStatus.Default : ComponentStatus.Disabled
@@ -115,12 +115,12 @@ const FluxQueryBuilder = ({
                   success
                     ? notifyCopyToClipboardSuccess(
                         null,
-                        'Query builder flux script has been copied to clipboard.',
+                        'Builder script has been copied to clipboard.',
                         ''
                       )
                     : notifyCopyToClipboardFailed(
                         null,
-                        'Query builder flux script was not copied to clipboard.',
+                        'Builder script was not copied to clipboard.',
                         ''
                       )
                 )
@@ -128,26 +128,12 @@ const FluxQueryBuilder = ({
                 e.preventDefault()
               }}
             />
-            <Button
-              size={ComponentSize.ExtraSmall}
-              color={ComponentColor.Primary}
-              onClick={() => {
-                try {
-                  const script = buildQuery(builderState)
-                  onSubmit(script)
-                } catch (ex) {
-                  console.error(ex)
-                  notify(
-                    fluxWizardError(
-                      'Unable to build flux script: ' + ex.message
-                    )
-                  )
-                }
-              }}
-              status={
-                isRunnable ? ComponentStatus.Default : ComponentStatus.Disabled
-              }
-              text="Submit"
+            <FluxQueryBuilderSubmit
+              isRunnable={isRunnable}
+              builderState={builderState}
+              editorScript={editorScript}
+              notify={notify}
+              onSubmit={onSubmit}
             />
           </div>
         </AggregationSelector>
diff --git a/ui/src/shared/components/TimeMachine/fluxQueryBuilder/FluxQueryBuilderSubmit.tsx b/ui/src/shared/components/TimeMachine/fluxQueryBuilder/FluxQueryBuilderSubmit.tsx
new file mode 100644
index 000000000..02293df04
--- /dev/null
+++ b/ui/src/shared/components/TimeMachine/fluxQueryBuilder/FluxQueryBuilderSubmit.tsx
@@ -0,0 +1,146 @@
+// Libraries
+import React, {useMemo, useRef, useState} from 'react'
+import {
+  Button,
+  ComponentColor,
+  ComponentSize,
+  ComponentStatus,
+} from 'src/reusable_ui'
+import {fluxWizardError} from 'src/shared/copy/notifications'
+import {PublishNotificationActionCreator} from 'src/types/actions/notifications'
+import {ClickOutside} from '../../ClickOutside'
+import {QueryBuilderState} from './types'
+import {buildQuery} from './util/generateFlux'
+
+interface Props {
+  isRunnable: boolean
+  onSubmit: (s: string) => void
+  editorScript: string
+  builderState: QueryBuilderState
+  notify: PublishNotificationActionCreator
+}
+const EMPTY_FN = () => {}
+
+const FluxQueryBuilderSubmit = ({
+  builderState,
+  isRunnable,
+  editorScript,
+  onSubmit,
+  notify,
+}: Props) => {
+  if (!isRunnable) {
+    return (
+      <Button
+        size={ComponentSize.ExtraSmall}
+        color={ComponentColor.Primary}
+        onClick={EMPTY_FN}
+        status={ComponentStatus.Disabled}
+        text="Submit"
+        customClass="fqb--submit"
+      />
+    )
+  }
+
+  const [showConfirm, setShowConfirm] = useState(false)
+  const buttonRef = useRef<HTMLDivElement>()
+  const lastConfirmedBuilderState = useMemo(() => {
+    return builderState
+  }, [editorScript])
+
+  return (
+    <div ref={buttonRef}>
+      {!showConfirm ? (
+        <Button
+          size={ComponentSize.ExtraSmall}
+          color={ComponentColor.Primary}
+          onClick={() => {
+            try {
+              const script = buildQuery(builderState)
+              const lastScript = buildQuery(lastConfirmedBuilderState)
+              // submit directly if editor is empty, the generated query is the same as the editor query
+              // or if the builder was used to generate the new script
+              if (
+                !editorScript ||
+                script === editorScript ||
+                editorScript === lastScript
+              ) {
+                onSubmit(script)
+              } else {
+                setShowConfirm(true)
+              }
+            } catch (ex) {
+              console.error(ex)
+              notify(
+                fluxWizardError('Unable to build flux script: ' + ex.message)
+              )
+            }
+          }}
+          status={ComponentStatus.Default}
+          text="Submit"
+          customClass="fqb--submit"
+        />
+      ) : (
+        <>
+          <Button
+            size={ComponentSize.ExtraSmall}
+            color={ComponentColor.Primary}
+            onClick={EMPTY_FN}
+            status={
+              isRunnable ? ComponentStatus.Default : ComponentStatus.Disabled
+            }
+            text="Submit"
+            customClass="fqb--submit"
+          />
+          <div
+            className="fqb--confirm-popup"
+            style={{
+              left: `${
+                buttonRef.current.getBoundingClientRect().right - 350
+              }px`,
+            }}
+          >
+            <span className="fqb--confirm-label">
+              Submitting the Script Builder will overwrite the existing Flux
+              script, any changes you have made using Flux will be discarded.
+              This cannot be recovered.
+            </span>
+            <ClickOutside onClickOutside={() => setShowConfirm(false)}>
+              <Button
+                size={ComponentSize.ExtraSmall}
+                color={ComponentColor.Danger}
+                onClick={() => {
+                  try {
+                    const script = buildQuery(builderState)
+                    setShowConfirm(false)
+                    onSubmit(script)
+                  } catch (ex) {
+                    console.error(ex)
+                    notify(
+                      fluxWizardError(
+                        'Unable to build flux script: ' + ex.message
+                      )
+                    )
+                  }
+                }}
+                status={ComponentStatus.Default}
+                text="OK"
+              />
+            </ClickOutside>
+          </div>
+          <span
+            className="fqb--confirm-caret"
+            style={{
+              left: `${
+                buttonRef.current.getBoundingClientRect().left +
+                buttonRef.current.getBoundingClientRect().width / 2
+              }px`,
+              top: `${buttonRef.current.getBoundingClientRect().bottom}px`,
+            }}
+          />
+        </>
+      )}
+    </div>
+  )
+}
+
+export default FluxQueryBuilderSubmit