diff --git a/packages/apidom-converter/src/strategies/openapi-3-1-to-openapi-3-0-3/refractor-plugins/security-scheme-type.ts b/packages/apidom-converter/src/strategies/openapi-3-1-to-openapi-3-0-3/refractor-plugins/security-scheme-type.ts
index 8d4ee74c3d..0088d45807 100644
--- a/packages/apidom-converter/src/strategies/openapi-3-1-to-openapi-3-0-3/refractor-plugins/security-scheme-type.ts
+++ b/packages/apidom-converter/src/strategies/openapi-3-1-to-openapi-3-0-3/refractor-plugins/security-scheme-type.ts
@@ -5,8 +5,18 @@ import {
   SecuritySchemeElement,
   isSecuritySchemeElement,
   isComponentsElement,
+  isReferenceElement,
+  mediaTypes,
 } from '@swagger-api/apidom-ns-openapi-3-1';
-import { AnnotationElement, toValue, isObjectElement, Element } from '@swagger-api/apidom-core';
+import {
+  Element,
+  ParseResultElement,
+  AnnotationElement,
+  isObjectElement,
+  toValue,
+  cloneDeep,
+} from '@swagger-api/apidom-core';
+import { dereferenceApiDOM, ReferenceSet, Reference, url } from '@swagger-api/apidom-reference';
 
 import type { Toolbox } from '../toolbox';
 
@@ -17,6 +27,9 @@ type SecuritySchemeTypePluginOptions = {
 const securitySchemeTypeRefractorPlugin =
   ({ annotations }: SecuritySchemeTypePluginOptions) =>
   (toolbox: Toolbox) => {
+    let parseResultElement: ParseResultElement | undefined;
+    const isRemovableSecuritySchemeElement = (value: unknown): value is SecuritySchemeElement =>
+      isSecuritySchemeElement(value) && toValue(value.type) === 'mutualTLS';
     const removedSecuritySchemes: SecuritySchemeElement[] = [];
     const createAnnotation = <T extends Element>(element: T) =>
       toolbox.createAnnotation.fromElement(
@@ -28,6 +41,9 @@ const securitySchemeTypeRefractorPlugin =
 
     return {
       visitor: {
+        ParseResultElement(element: ParseResultElement) {
+          parseResultElement = element;
+        },
         OpenApi3_1Element(element: OpenApi3_1Element) {
           if (!isComponentsElement(element.components)) return undefined;
           if (!isObjectElement(element.components.securitySchemes)) return undefined;
@@ -40,11 +56,43 @@ const securitySchemeTypeRefractorPlugin =
 
           return undefined;
         },
-        ComponentsElement(element: ComponentsElement) {
+        async ComponentsElement(element: ComponentsElement) {
           if (!isObjectElement(element.securitySchemes)) return undefined;
 
+          /**
+           * Removing Reference Objects pointing to removable Security Scheme Objects.
+           * We need to remove Reference Objects first as they might be pointing
+           * to Security Scheme Objects that are going to be removed.
+           */
+          const baseURI = url.cwd();
+          const rootReference = Reference({ uri: baseURI, value: cloneDeep(parseResultElement!) });
+          for (const memberElement of element.securitySchemes) {
+            if (!isReferenceElement(memberElement.value)) continue; // eslint-disable-line no-continue
+
+            const { value: referenceElement } = memberElement;
+            const reference = Reference({
+              uri: `${baseURI}#reference`,
+              value: new ParseResultElement([referenceElement]),
+            });
+            const refSet = ReferenceSet({ refs: [reference, rootReference] });
+            // eslint-disable-next-line no-await-in-loop
+            const dereferenced = await dereferenceApiDOM(referenceElement, {
+              resolve: { baseURI: reference.uri },
+              parse: { mediaType: mediaTypes.latest() },
+              dereference: { refSet, immutable: false },
+            });
+
+            if (isRemovableSecuritySchemeElement(dereferenced)) {
+              element.securitySchemes.remove(toValue(memberElement.key));
+              annotations.push(createAnnotation(referenceElement));
+            }
+          }
+
+          /**
+           * Removing Security Scheme Objects.
+           */
           element.securitySchemes.forEach((value, key) => {
-            if (isSecuritySchemeElement(value) && toValue(value.type) === 'mutualTLS') {
+            if (isRemovableSecuritySchemeElement(value)) {
               if (!removedSecuritySchemes.includes(value)) removedSecuritySchemes.push(value);
               (element.securitySchemes as SecuritySchemeElement).remove(toValue(key));
               annotations.push(createAnnotation(value));
@@ -80,6 +128,7 @@ const securitySchemeTypeRefractorPlugin =
       },
       post() {
         removedSecuritySchemes.length = 0;
+        parseResultElement = undefined;
       },
     };
   };
diff --git a/packages/apidom-converter/test/strategies/openapi-3-1-to-openapi-3-0-3/refractor-plugins/security-scheme-type/__snapshots__/index.ts.snap b/packages/apidom-converter/test/strategies/openapi-3-1-to-openapi-3-0-3/refractor-plugins/security-scheme-type/__snapshots__/index.ts.snap
index a7b5072af9..5492069e5f 100644
--- a/packages/apidom-converter/test/strategies/openapi-3-1-to-openapi-3-0-3/refractor-plugins/security-scheme-type/__snapshots__/index.ts.snap
+++ b/packages/apidom-converter/test/strategies/openapi-3-1-to-openapi-3-0-3/refractor-plugins/security-scheme-type/__snapshots__/index.ts.snap
@@ -1,5 +1,50 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
+exports[`converter strategies openapi-3-1-to-openapi-3-0-3 security-scheme-type should remove Reference Objects pointing to removable Security Scheme Objects 1`] = `
+{
+  "openapi": "3.0.3",
+  "paths": {
+    "/foo": {
+      "get": {
+        "summary": "foo",
+        "operationId": "foo",
+        "security": [
+          {
+            "mutualTLS-scheme2": [
+              "read",
+              "write"
+            ]
+          },
+          {
+            "oauth2-scheme2": [
+              "read",
+              "write"
+            ]
+          }
+        ],
+        "responses": {
+          "200": {
+            "description": "foo"
+          }
+        }
+      }
+    }
+  },
+  "components": {
+    "securitySchemes": {
+      "apiKey-scheme1": {
+        "$ref": "#/components/securitySchemes/apiKey-scheme2"
+      },
+      "apiKey-scheme2": {
+        "type": "oauth2",
+        "name": "oauth2-scheme",
+        "in": "header"
+      }
+    }
+  }
+}
+`;
+
 exports[`converter strategies openapi-3-1-to-openapi-3-0-3 security-scheme-type should remove SecurityScheme object if it has "mutualTLS" type 1`] = `
 {
   "openapi": "3.0.3",
diff --git a/packages/apidom-converter/test/strategies/openapi-3-1-to-openapi-3-0-3/refractor-plugins/security-scheme-type/fixtures/reference-objects.json b/packages/apidom-converter/test/strategies/openapi-3-1-to-openapi-3-0-3/refractor-plugins/security-scheme-type/fixtures/reference-objects.json
new file mode 100644
index 0000000000..1d31198582
--- /dev/null
+++ b/packages/apidom-converter/test/strategies/openapi-3-1-to-openapi-3-0-3/refractor-plugins/security-scheme-type/fixtures/reference-objects.json
@@ -0,0 +1,50 @@
+{
+  "openapi": "3.1.0",
+  "paths": {
+    "/foo": {
+      "get": {
+        "summary": "foo",
+        "operationId": "foo",
+        "security": [
+          {
+            "mutualTLS-scheme2": [
+              "read",
+              "write"
+            ]
+          },
+          {
+            "oauth2-scheme2": [
+              "read",
+              "write"
+            ]
+          }
+        ],
+        "responses": {
+          "200": {
+            "description": "foo"
+          }
+        }
+      }
+    }
+  },
+  "components": {
+    "securitySchemes": {
+      "mutualTLS-scheme1": {
+        "$ref": "#/components/securitySchemes/mutualTLS-scheme2"
+      },
+      "apiKey-scheme1": {
+        "$ref": "#/components/securitySchemes/apiKey-scheme2"
+      },
+      "mutualTLS-scheme2": {
+        "type": "mutualTLS",
+        "name": "mutualTLS-scheme",
+        "in": "header"
+      },
+      "apiKey-scheme2": {
+        "type": "oauth2",
+        "name": "oauth2-scheme",
+        "in": "header"
+      }
+    }
+  }
+}
diff --git a/packages/apidom-converter/test/strategies/openapi-3-1-to-openapi-3-0-3/refractor-plugins/security-scheme-type/index.ts b/packages/apidom-converter/test/strategies/openapi-3-1-to-openapi-3-0-3/refractor-plugins/security-scheme-type/index.ts
index 425d7b5953..891ffbcc83 100644
--- a/packages/apidom-converter/test/strategies/openapi-3-1-to-openapi-3-0-3/refractor-plugins/security-scheme-type/index.ts
+++ b/packages/apidom-converter/test/strategies/openapi-3-1-to-openapi-3-0-3/refractor-plugins/security-scheme-type/index.ts
@@ -73,6 +73,21 @@ describe('converter', function () {
           assert.strictEqual(endColumn, 13);
           assert.strictEqual(endChar, 247);
         });
+
+        specify(
+          'should remove Reference Objects pointing to removable Security Scheme Objects',
+          async function () {
+            const fixturePath = path.join(__dirname, 'fixtures', 'reference-objects.json');
+            const convertedParseResult = await convert(fixturePath, {
+              convert: {
+                sourceMediaType: openAPI31MediaTypes.findBy('3.1.0', 'json'),
+                targetMediaType: openAPI30MediaTypes.findBy('3.0.3', 'json'),
+              },
+            });
+
+            expect(toJSON(convertedParseResult.api!, undefined, 2)).toMatchSnapshot();
+          },
+        );
       });
     });
   });