diff --git a/src/platform/plugins/shared/workflows_management/common/lib/yaml/update_workflow_yaml_fields.test.ts b/src/platform/plugins/shared/workflows_management/common/lib/yaml/update_workflow_yaml_fields.test.ts
index d91111d0bb942..f9e285867e10e 100644
--- a/src/platform/plugins/shared/workflows_management/common/lib/yaml/update_workflow_yaml_fields.test.ts
+++ b/src/platform/plugins/shared/workflows_management/common/lib/yaml/update_workflow_yaml_fields.test.ts
@@ -63,6 +63,52 @@ steps: []`;
     expect(result).toContain('enabled: false');
   });
 
+  it('should preserve comments, blank lines, and formatting when toggling enabled', () => {
+    const yaml = `# Workflow configuration
+name: Test Workflow
+
+# Whether the workflow is active
+enabled: false
+
+steps:
+  # Create a Jira ticket
+  - name: step1
+    type: jira
+    params:
+      summary: test`;
+    const workflow: Partial<EsWorkflow> = { enabled: true };
+
+    const result = updateWorkflowYamlFields(yaml, workflow, true);
+
+    expect(result).toContain('enabled: true');
+    expect(result).not.toContain('enabled: false');
+    expect(result).toContain('# Workflow configuration');
+    expect(result).toContain('# Whether the workflow is active');
+    expect(result).toContain('# Create a Jira ticket');
+    const blankLineCount = (result.match(/\n\n/g) || []).length;
+    expect(blankLineCount).toBeGreaterThanOrEqual(2);
+    expect(result).toContain('name: Test Workflow');
+    expect(result).toContain('summary: test');
+  });
+
+  it('should preserve quoted template expressions when toggling enabled', () => {
+    const yaml = `name: Test Workflow
+enabled: false
+steps:
+  - name: step1
+    type: jira
+    params:
+      comment: "{{ inputs.comment }}"
+      summary: "{{ inputs.summary }}"`;
+    const workflow: Partial<EsWorkflow> = { enabled: true };
+
+    const result = updateWorkflowYamlFields(yaml, workflow, true);
+
+    expect(result).toContain('enabled: true');
+    expect(result).toContain('comment: "{{ inputs.comment }}"');
+    expect(result).toContain('summary: "{{ inputs.summary }}"');
+  });
+
   it('should use enabledValue parameter when provided', () => {
     const yaml = 'name: Test Workflow\nenabled: true\nsteps: []';
     const workflow: Partial<EsWorkflow> = { enabled: true }; // Request to enable
diff --git a/src/platform/plugins/shared/workflows_management/common/lib/yaml/update_yaml_field.test.ts b/src/platform/plugins/shared/workflows_management/common/lib/yaml/update_yaml_field.test.ts
index 1e4f542a77d3e..efb2962266f6d 100644
--- a/src/platform/plugins/shared/workflows_management/common/lib/yaml/update_yaml_field.test.ts
+++ b/src/platform/plugins/shared/workflows_management/common/lib/yaml/update_yaml_field.test.ts
@@ -138,6 +138,64 @@ steps:
     expect(result).toContain('- name: step1');
   });
 
+  it('should preserve comments, blank lines, and formatting when toggling enabled', () => {
+    const yaml = `# Workflow configuration
+name: Test Workflow
+description: A workflow that does things
+
+# Whether the workflow is active
+enabled: false
+
+steps:
+  # Create a Jira ticket
+  - name: step1
+    type: jira
+    params:
+      summary: test
+
+  # Notify the user
+  - name: step2
+    type: slack
+    params:
+      channel: general`;
+
+    const result = updateYamlField(yaml, 'enabled', true);
+
+    // Only the enabled value should change
+    expect(result).toContain('enabled: true');
+    expect(result).not.toContain('enabled: false');
+
+    // All comments preserved
+    expect(result).toContain('# Workflow configuration');
+    expect(result).toContain('# Whether the workflow is active');
+    expect(result).toContain('# Create a Jira ticket');
+    expect(result).toContain('# Notify the user');
+
+    // Blank lines preserved
+    const blankLineCount = (result.match(/\n\n/g) || []).length;
+    expect(blankLineCount).toBeGreaterThanOrEqual(3);
+
+    // Rest of content unchanged
+    expect(result).toContain('name: Test Workflow');
+    expect(result).toContain('description: A workflow that does things');
+    expect(result).toContain('channel: general');
+  });
+
+  it('should preserve template expressions like {{ inputs.comment }}', () => {
+    const yaml = `name: Test Workflow
+enabled: false
+steps:
+  - name: step1
+    type: jira
+    params:
+      comment: "{{ inputs.comment }}"`;
+
+    const result = updateYamlField(yaml, 'enabled', true);
+
+    expect(result).toContain('enabled: true');
+    expect(result).toContain('comment: "{{ inputs.comment }}"');
+  });
+
   it('should handle nested field paths with dot notation', () => {
     const yaml = `metadata:
   version: 1.0
diff --git a/src/platform/plugins/shared/workflows_management/server/workflows_management/workflows_management_service.test.ts b/src/platform/plugins/shared/workflows_management/server/workflows_management/workflows_management_service.test.ts
index a5e08210f0654..ac3a4047cdffa 100644
--- a/src/platform/plugins/shared/workflows_management/server/workflows_management/workflows_management_service.test.ts
+++ b/src/platform/plugins/shared/workflows_management/server/workflows_management/workflows_management_service.test.ts
@@ -1486,6 +1486,76 @@ steps:
         })
       );
     });
+
+    it('should preserve YAML comments, formatting, and template expressions when toggling enabled', async () => {
+      const mockRequest = {
+        auth: {
+          credentials: { username: 'test-user' },
+        },
+      } as any;
+
+      const yamlWithComments = `# Workflow configuration
+name: Test Workflow
+description: A test workflow
+
+# Whether the workflow is active
+enabled: false
+
+triggers:
+  - type: manual
+
+steps:
+  # Create a Jira ticket
+  - type: console
+    name: first-step
+    with:
+      message: "{{ inputs.comment }}"`;
+
+      const existingDoc = {
+        _id: 'test-workflow-id',
+        _source: {
+          ...mockWorkflowDocument._source,
+          enabled: false,
+          yaml: yamlWithComments,
+          definition: {
+            name: 'Test Workflow',
+            enabled: false,
+            triggers: [{ type: 'manual' }],
+            steps: [
+              {
+                type: 'console',
+                name: 'first-step',
+                with: { message: '{{ inputs.comment }}' },
+              },
+            ],
+          },
+        },
+      };
+
+      mockEsClient.search.mockResolvedValue({ hits: { hits: [existingDoc] } } as any);
+
+      // Toggle enabled without providing yaml (metadata-only update)
+      await service.updateWorkflow('test-workflow-id', { enabled: true }, 'default', mockRequest);
+
+      const indexCall = mockEsClient.index.mock.calls[0][0] as any;
+      const savedYaml = indexCall.document.yaml;
+
+      // enabled should be toggled
+      expect(savedYaml).toContain('enabled: true');
+      expect(savedYaml).not.toContain('enabled: false');
+
+      // Comments should be preserved
+      expect(savedYaml).toContain('# Workflow configuration');
+      expect(savedYaml).toContain('# Whether the workflow is active');
+      expect(savedYaml).toContain('# Create a Jira ticket');
+
+      // Template expressions should not be corrupted
+      expect(savedYaml).toContain('{{ inputs.comment }}');
+      expect(savedYaml).not.toContain('null');
+
+      // Blank lines should be preserved
+      expect((savedYaml.match(/\n\n/g) || []).length).toBeGreaterThanOrEqual(2);
+    });
   });
 
   describe('deleteWorkflows', () => {
diff --git a/src/platform/plugins/shared/workflows_management/server/workflows_management/workflows_management_service.ts b/src/platform/plugins/shared/workflows_management/server/workflows_management/workflows_management_service.ts
index b65381e6e9a40..deff5d97f30bc 100644
--- a/src/platform/plugins/shared/workflows_management/server/workflows_management/workflows_management_service.ts
+++ b/src/platform/plugins/shared/workflows_management/server/workflows_management/workflows_management_service.ts
@@ -69,11 +69,7 @@ import {
 } from '../../common/lib/errors';
 
 import { validateStepNameUniqueness } from '../../common/lib/validate_step_names';
-import {
-  parseWorkflowYamlToJSON,
-  parseYamlToJSONWithoutValidation,
-  stringifyWorkflowDefinition,
-} from '../../common/lib/yaml';
+import { parseWorkflowYamlToJSON, updateWorkflowYamlFields } from '../../common/lib/yaml';
 import { getWorkflowZodSchema } from '../../common/schema';
 import { getAuthenticatedUser } from '../lib/get_user';
 import { hasScheduledTriggers } from '../lib/schedule_utils';
@@ -531,23 +527,17 @@ export class WorkflowsService {
         }
 
         if (yamlUpdated && existingDocument._source?.yaml) {
-          const originalYamlParse = parseYamlToJSONWithoutValidation(existingDocument._source.yaml);
-          const baseDefinition = originalYamlParse.success
-            ? originalYamlParse.json
-            : existingDocument._source?.definition;
-
-          if (baseDefinition) {
-            const fieldUpdates = {
-              ...(workflow.name !== undefined && { name: workflow.name }),
-              ...(workflow.enabled !== undefined && { enabled: updatedData.enabled }),
-              ...(workflow.description !== undefined && { description: workflow.description }),
-              ...(workflow.tags !== undefined && { tags: workflow.tags }),
-            };
-            updatedData.yaml = stringifyWorkflowDefinition({
-              ...baseDefinition,
-              ...fieldUpdates,
-            });
-          }
+          // Use in-place YAML field updates to preserve formatting, comments,
+          // and template expressions that would be corrupted by a parse-to-JSON then re-stringify cycle.
+          // `enabledValue` is passed separately because the server may override
+          // the requested value (e.g. force `false` when the workflow has no valid
+          // definition). Other fields (name, description, tags) are read directly
+          // from the `workflow` object inside `updateWorkflowYamlFields`.
+          updatedData.yaml = updateWorkflowYamlFields(
+            existingDocument._source.yaml,
+            workflow,
+            updatedData.enabled
+          );
         }
       }