diff --git a/packages/apollo-federation/CHANGELOG.md b/packages/apollo-federation/CHANGELOG.md
index 6673974e47a..88dd6d4a5a0 100644
--- a/packages/apollo-federation/CHANGELOG.md
+++ b/packages/apollo-federation/CHANGELOG.md
@@ -4,7 +4,7 @@
 
 > The changes noted within this `vNEXT` section have not been released yet.  New PRs and commits which introduce changes should include an entry in this `vNEXT` section as part of their development.  When a release is being prepared, a new header will be (manually) created below and the the appropriate changes within that release will be moved into the new section.
 
-- _Nothing yet! Stay tuned._
+- Fix `v0.12.0` regression: Preserve the `@deprecated` type-system directive as a special case when removing type system directives during composition, resolving an unintentional breaking change introduced by [#3736](https://github.com/apollographql/apollo-server/pull/3736). [#3792](https://github.com/apollographql/apollo-server/pull/3792)
 
 ## v0.12.0
 
diff --git a/packages/apollo-federation/src/composition/__tests__/composeAndValidate.test.ts b/packages/apollo-federation/src/composition/__tests__/composeAndValidate.test.ts
index f3e20cec8bf..9cb3206d71e 100644
--- a/packages/apollo-federation/src/composition/__tests__/composeAndValidate.test.ts
+++ b/packages/apollo-federation/src/composition/__tests__/composeAndValidate.test.ts
@@ -623,4 +623,32 @@ describe('composition of schemas with directives', () => {
       `societal: String!`,
     );
   });
+
+  it(`doesn't strip the special case @deprecated type-system directive`, () => {
+    const serviceA = {
+      typeDefs: gql`
+        type EarthConcern {
+          environmental: String!
+        }
+
+        extend type Query {
+          importantDirectives: [EarthConcern!]!
+            @deprecated(reason: "Don't remove me please")
+        }
+      `,
+      name: 'serviceA',
+    };
+
+    const { schema, errors } = composeAndValidate([serviceA]);
+    expect(errors).toHaveLength(0);
+
+    const deprecated = schema.getDirective('deprecated');
+    expect(deprecated).toMatchInlineSnapshot(`"@deprecated"`);
+
+    const queryType = schema.getType('Query') as GraphQLObjectType;
+    const field = queryType.getFields()['importantDirectives'];
+
+    expect(field.isDeprecated).toBe(true);
+    expect(field.deprecationReason).toEqual("Don't remove me please");
+  });
 });
diff --git a/packages/apollo-federation/src/composition/utils.ts b/packages/apollo-federation/src/composition/utils.ts
index 34ca9b06aa8..9422f29c102 100644
--- a/packages/apollo-federation/src/composition/utils.ts
+++ b/packages/apollo-federation/src/composition/utils.ts
@@ -86,6 +86,9 @@ export function stripExternalFieldsFromTypeDefs(
 export function stripTypeSystemDirectivesFromTypeDefs(typeDefs: DocumentNode) {
   const typeDefsWithoutTypeSystemDirectives = visit(typeDefs, {
     Directive(node) {
+      // The `deprecated` directive is an exceptional case that we want to leave in
+      if (node.name.value === 'deprecated') return;
+
       const isFederationDirective = federationDirectives.some(
         ({ name }) => name === node.name.value,
       );