diff --git a/web/pgadmin/static/js/components/ReactCodeMirror/CustomEditorView.js b/web/pgadmin/static/js/components/ReactCodeMirror/CustomEditorView.js
index b48f77a92..5708e1fe5 100644
--- a/web/pgadmin/static/js/components/ReactCodeMirror/CustomEditorView.js
+++ b/web/pgadmin/static/js/components/ReactCodeMirror/CustomEditorView.js
@@ -27,7 +27,9 @@ function getAutocompLoading({ bottom, left }, dom) {
 export default class CustomEditorView extends EditorView {
   constructor(...args) {
     super(...args);
+    // Set the initial and clean state for the document and EOL(end of line).
     this._cleanDoc = this.state.doc;
+    this._cleanDocEOL = this.getEOL();
   }
 
   getValue(tillCursor=false, useLineSep=false) {
@@ -268,10 +270,12 @@ export default class CustomEditorView extends EditorView {
 
   markClean() {
     this._cleanDoc = this.state.doc;
+    this._cleanDocEOL = this.getEOL(); // Update the initial EOL value.
   }
 
   isDirty() {
-    return !this._cleanDoc.eq(this.state.doc);
+    // Return true if either the document content or the EOL(end of line) has changed.
+    return !this._cleanDoc.eq(this.state.doc) || this._cleanDocEOL !== this.getEOL();
   }
 
   fireDOMEvent(event) {
@@ -340,4 +344,11 @@ export default class CustomEditorView extends EditorView {
       effects: eolCompartment.reconfigure(eol.of(val))
     });
   }
+
+  // Use to detect EOL type.
+  detectEOL(content) {
+    const lineSep = content.includes('\r\n') ? '\r\n' : '\n';
+    this.setEOL(lineSep);
+    return lineSep == '\r\n' ? 'crlf' : 'lf';
+  }
 }
diff --git a/web/pgadmin/tools/sqleditor/static/js/components/QueryToolComponent.jsx b/web/pgadmin/tools/sqleditor/static/js/components/QueryToolComponent.jsx
index 0c7d6bf52..4f0ac6482 100644
--- a/web/pgadmin/tools/sqleditor/static/js/components/QueryToolComponent.jsx
+++ b/web/pgadmin/tools/sqleditor/static/js/components/QueryToolComponent.jsx
@@ -271,7 +271,7 @@ export default function QueryToolComponent({params, pgWindow, pgAdmin, selectedN
             {
               maximizable: true,
               tabs: [
-                LayoutDocker.getPanel({id: PANELS.QUERY, title: gettext('Query'), content: <Query  onTextSelect={(text) => setSelectedText(text)} handleEndOfLineChange={handleEndOfLineChange}/>}),
+                LayoutDocker.getPanel({id: PANELS.QUERY, title: gettext('Query'), content: <Query  onTextSelect={(text) => setSelectedText(text)} setQtStatePartial={setQtStatePartial}/>}),
                 LayoutDocker.getPanel({id: PANELS.HISTORY, title: gettext('Query History'), content: <QueryHistory />,
                   cached: undefined}),
               ],
diff --git a/web/pgadmin/tools/sqleditor/static/js/components/sections/Query.jsx b/web/pgadmin/tools/sqleditor/static/js/components/sections/Query.jsx
index c8f650c52..277fdabc2 100644
--- a/web/pgadmin/tools/sqleditor/static/js/components/sections/Query.jsx
+++ b/web/pgadmin/tools/sqleditor/static/js/components/sections/Query.jsx
@@ -10,7 +10,7 @@ import React, {useContext, useCallback, useEffect, useMemo } from 'react';
 import { format } from 'sql-formatter';
 import { QueryToolContext, QueryToolEventsContext } from '../QueryToolComponent';
 import CodeMirror from '../../../../../../static/js/components/ReactCodeMirror';
-import {OS_EOL, PANELS, QUERY_TOOL_EVENTS} from '../QueryToolConstants';
+import { PANELS, QUERY_TOOL_EVENTS} from '../QueryToolConstants';
 import url_for from 'sources/url_for';
 import { LayoutDockerContext, LAYOUT_EVENTS } from '../../../../../../static/js/helpers/Layout';
 import ConfirmSaveContent from '../../../../../../static/js/Dialogs/ConfirmSaveContent';
@@ -56,7 +56,7 @@ async function registerAutocomplete(editor, api, transId) {
   });
 }
 
-export default function Query({onTextSelect, handleEndOfLineChange}) {
+export default function Query({onTextSelect, setQtStatePartial}) {
   const editor = React.useRef();
   const eventBus = useContext(QueryToolEventsContext);
   const queryToolCtx = useContext(QueryToolContext);
@@ -187,12 +187,13 @@ export default function Query({onTextSelect, handleEndOfLineChange}) {
         editor.current.setValue(res.data);
         //Check the file content for Trojan Source
         checkTrojanSource(res.data);
-        editor.current.markClean();
         eventBus.fireEvent(QUERY_TOOL_EVENTS.LOAD_FILE_DONE, fileName, true);
-        const lineSep = res.data.includes('\r\n') ? 'crlf' : 'lf';
-        if (lineSep !== OS_EOL){
-          handleEndOfLineChange(lineSep);
-        }
+        // Detect line separator from content and editor's EOL.
+        const lineSep = editor.current?.detectEOL(res.data);
+        // Update the EOL if it differs from the current editor EOL
+        setQtStatePartial({ eol: lineSep });
+        // Mark the editor content as clean
+        editor.current?.markClean();
       }).catch((err)=>{
         eventBus.fireEvent(QUERY_TOOL_EVENTS.LOAD_FILE_DONE, null, false);
         pgAdmin.Browser.notifier.error(parseApiError(err));
@@ -292,8 +293,9 @@ export default function Query({onTextSelect, handleEndOfLineChange}) {
     });
 
     eventBus.registerListener(QUERY_TOOL_EVENTS.CHANGE_EOL, (lineSep)=>{
+      // Set the new EOL character in the editor.
       editor.current?.setEOL(lineSep);
-      eventBus.fireEvent(QUERY_TOOL_EVENTS.QUERY_CHANGED, true);
+      eventBus.fireEvent(QUERY_TOOL_EVENTS.QUERY_CHANGED, editor.current?.isDirty());    
     });
 
     eventBus.registerListener(QUERY_TOOL_EVENTS.EDITOR_TOGGLE_CASE, ()=>{
@@ -526,5 +528,5 @@ export default function Query({onTextSelect, handleEndOfLineChange}) {
 
 Query.propTypes = {
   onTextSelect: PropTypes.func,
-  handleEndOfLineChange: PropTypes.func
+  setQtStatePartial: PropTypes.func
 };