diff --git a/src/components/configuration/FieldProfilePopover.tsx b/src/components/configuration/FieldProfilePopover.tsx
index f495d964..bc59b730 100644
--- a/src/components/configuration/FieldProfilePopover.tsx
+++ b/src/components/configuration/FieldProfilePopover.tsx
@@ -5,11 +5,11 @@ import type * as t from '@/types';
 import { ProfileValueModal, getDefaultValue } from './ProfileValueModal';
 import { DeleteProfileValueModal } from './DeleteProfileValueModal';
 import { EditButton, TrashButton } from '@/components/shared';
+import { getControlType, serializeModalValue } from './utils';
 import { useProfileMutations, useLocalize } from '@/hooks';
 import { availableScopesOptions } from '@/server';
 import { getScopeTypeConfig } from '@/constants';
-import { serializeKVPairs, cn } from '@/utils';
-import { getControlType } from './utils';
+import { cn } from '@/utils';
 
 export function FieldProfilePopover({
   fieldPath,
@@ -71,7 +71,7 @@ export function FieldProfilePopover({
 
   const handleModalSave = useCallback(() => {
     if (modalIsBase && onBaseValueChange) {
-      onBaseValueChange(serializeKVPairs(modalValue));
+      onBaseValueChange(serializeModalValue(controlType, modalValue));
       setModalOpen(false);
       setModalIsBase(false);
       return;
@@ -81,7 +81,7 @@ export function FieldProfilePopover({
       {
         principalType: modalScope.principalType,
         principalId: modalScope.principalId,
-        value: serializeKVPairs(modalValue),
+        value: serializeModalValue(controlType, modalValue),
       },
       {
         onSuccess: () => {
@@ -94,7 +94,7 @@ export function FieldProfilePopover({
         },
       },
     );
-  }, [modalIsBase, modalScope, modalValue, modalMode, saveMutation, onBaseValueChange]);
+  }, [modalIsBase, modalScope, modalValue, modalMode, controlType, saveMutation, onBaseValueChange]);
 
   const handleModalCancel = useCallback(() => {
     setModalOpen(false);
diff --git a/src/components/configuration/FieldRenderer.test.tsx b/src/components/configuration/FieldRenderer.test.tsx
index 8a23a885..c04123ba 100644
--- a/src/components/configuration/FieldRenderer.test.tsx
+++ b/src/components/configuration/FieldRenderer.test.tsx
@@ -215,6 +215,22 @@ describe('SingleFieldRenderer', () => {
     expect(screen.getByDisplayValue('Authorization')).toBeInTheDocument();
     expect(screen.getByDisplayValue('Bearer token')).toBeInTheDocument();
   });
+
+  it('emits an empty record, not an empty array, when the last key-value row is removed', () => {
+    const field = createField({ key: 'headers', type: 'record' });
+    const onChange = vi.fn();
+    render(
+      <SingleFieldRenderer
+        field={field}
+        value={{ Authorization: 'Bearer token' }}
+        path="section.headers"
+        getValue={getValue}
+        onChange={onChange}
+      />,
+    );
+    fireEvent.click(screen.getByRole('button', { name: 'com_ui_delete com_ui_entry 1' }));
+    expect(onChange).toHaveBeenCalledWith('section.headers', {});
+  });
 });
 
 describe('FieldRenderer with imported config values', () => {
diff --git a/src/components/configuration/FieldRenderer.tsx b/src/components/configuration/FieldRenderer.tsx
index bc1e6d0b..ac07de07 100644
--- a/src/components/configuration/FieldRenderer.tsx
+++ b/src/components/configuration/FieldRenderer.tsx
@@ -10,6 +10,7 @@ import {
   getControlType,
   getEnumOptions,
   hasDescendant,
+  kvPairsEditValue,
   toKVPair,
   isStringLikeItemType,
   splitUnionTypes,
@@ -23,6 +24,7 @@ import { ListRecordField } from './fields/ListRecordField';
 import { renderCollapsible } from './renderCollapsible';
 import { TextareaField } from './fields/TextareaField';
 import { KeyValueField } from './fields/KeyValueField';
+import { cn, getSecretPreviewValue } from '@/utils';
 import { NumberField } from './fields/NumberField';
 import { SecretField } from './fields/SecretField';
 import { ToggleField } from './fields/ToggleField';
@@ -32,7 +34,6 @@ import { ListField } from './fields/ListField';
 import { CodeField } from './fields/CodeField';
 import { ConfigRow } from './ConfigRow';
 import { useLocalize } from '@/hooks';
-import { cn, getSecretPreviewValue } from '@/utils';
 
 function formatDefault(value: t.ConfigValue): string | null {
   if (value === undefined || value === null) return null;
@@ -477,7 +478,7 @@ export function SingleFieldRenderer({
         <KeyValueField
           id={fieldId}
           pairs={pairs}
-          onChange={(newPairs) => onChange(path, newPairs)}
+          onChange={(newPairs) => onChange(path, kvPairsEditValue(newPairs))}
           disabled={disabled}
           valueTypes={field.recordValueKVTypes}
           aria-label={fieldLabel}
@@ -1221,7 +1222,7 @@ export function renderInlineField(
         <KeyValueField
           id={fieldId}
           pairs={pairs}
-          onChange={(p) => onChange(field.key, p)}
+          onChange={(p) => onChange(field.key, kvPairsEditValue(p))}
           disabled={disabled}
           valueTypes={field.recordValueKVTypes}
           aria-label={fieldLabel}
diff --git a/src/components/configuration/ProfileValueModal.test.tsx b/src/components/configuration/ProfileValueModal.test.tsx
new file mode 100644
index 00000000..8d6a7685
--- /dev/null
+++ b/src/components/configuration/ProfileValueModal.test.tsx
@@ -0,0 +1,85 @@
+import { vi, describe, it, expect } from 'vitest';
+import { render, screen, fireEvent } from '@testing-library/react';
+import type * as t from '@/types';
+import { ProfileValueModal, getDefaultValue } from './ProfileValueModal';
+import { createField } from '@/test/fixtures';
+
+vi.mock('@/hooks/useLocalize', () => ({
+  default: () => (key: string) => key,
+  useLocalize: () => (key: string) => key,
+}));
+
+interface ChildrenProps {
+  children?: React.ReactNode;
+}
+interface ButtonProps {
+  label?: string;
+  onClick?: () => void;
+}
+interface IconButtonProps {
+  icon: string;
+  onClick?: () => void;
+  'aria-label'?: string;
+}
+
+vi.mock('@clickhouse/click-ui', () => ({
+  Icon: () => null,
+  Button: ({ label, onClick }: ButtonProps) => <button onClick={onClick}>{label}</button>,
+  IconButton: ({ icon, onClick, ...props }: IconButtonProps) => (
+    <button onClick={onClick} aria-label={props['aria-label'] ?? icon} />
+  ),
+  Select: Object.assign(({ children }: ChildrenProps) => <div>{children}</div>, {
+    Item: ({ children }: ChildrenProps) => <div>{children}</div>,
+  }),
+  Dialog: Object.assign(({ children }: ChildrenProps) => <div>{children}</div>, {
+    Content: ({ children }: ChildrenProps) => <div>{children}</div>,
+  }),
+}));
+
+describe('getDefaultValue', () => {
+  it('returns an empty record for record fields so an untouched save stays object-typed', () => {
+    expect(getDefaultValue('record')).toEqual({});
+  });
+
+  it('returns an empty array for array fields', () => {
+    expect(getDefaultValue('array')).toEqual([]);
+  });
+});
+
+describe('ProfileValueModal — record fields', () => {
+  function renderModal(value: t.ConfigValue, onChange: (v: t.ConfigValue) => void) {
+    return render(
+      <ProfileValueModal
+        open
+        fieldSchema={createField({ key: 'headers', type: 'record' })}
+        controlType="record"
+        value={value}
+        onChange={onChange}
+        onSave={() => {}}
+        onCancel={() => {}}
+        saving={false}
+        scopeName="Base configuration"
+        scopeType="BASE"
+        mode="edit"
+      />,
+    );
+  }
+
+  it('emits an empty record, not an empty array, when the last row is removed', () => {
+    const onChange = vi.fn();
+    renderModal({ Authorization: 'Bearer token' }, onChange);
+    fireEvent.click(screen.getByRole('button', { name: 'com_ui_delete com_ui_entry 1' }));
+    expect(onChange).toHaveBeenCalledWith({});
+  });
+
+  it('keeps in-progress rows as raw pairs while editing', () => {
+    const onChange = vi.fn();
+    renderModal({ Authorization: 'Bearer token' }, onChange);
+    const valueInput = screen.getByLabelText('com_ui_value 1');
+    fireEvent.change(valueInput, { target: { value: 'Bearer {{API_KEY}}' } });
+    fireEvent.blur(valueInput);
+    expect(onChange).toHaveBeenCalledWith([
+      { key: 'Authorization', value: 'Bearer {{API_KEY}}', valueType: 'string' },
+    ]);
+  });
+});
diff --git a/src/components/configuration/ProfileValueModal.tsx b/src/components/configuration/ProfileValueModal.tsx
index 560bbf65..0f8f4c6a 100644
--- a/src/components/configuration/ProfileValueModal.tsx
+++ b/src/components/configuration/ProfileValueModal.tsx
@@ -2,7 +2,7 @@ import { useState } from 'react';
 import { PrincipalType } from 'librechat-data-provider';
 import { Icon, Button, Dialog } from '@clickhouse/click-ui';
 import type * as t from '@/types';
-import { getEnumOptions, getArrayItemType, toKVPair } from './utils';
+import { getEnumOptions, getArrayItemType, kvPairsEditValue, toKVPair } from './utils';
 import { KeyValueField } from './fields/KeyValueField';
 import { TrashButton } from '@/components/shared';
 import { getScopeTypeConfig } from '@/constants';
@@ -208,7 +208,7 @@ function ModalValueControl({
       <KeyValueField
         id="profile-kv"
         pairs={pairs}
-        onChange={onChange}
+        onChange={(p) => onChange(kvPairsEditValue(p))}
         aria-label={localize('com_ui_value')}
       />
     );
@@ -318,7 +318,7 @@ export function getDefaultValue(controlType: string, fieldSchema?: t.SchemaField
     return opts.length > 0 ? opts[0].value : '';
   }
   if (controlType === 'array') return [];
-  if (controlType === 'record') return [];
+  if (controlType === 'record') return {};
   if (controlType === 'object' || controlType === 'code') return {};
   return '';
 }
diff --git a/src/components/configuration/sections/__tests__/McpServersRenderer.test.tsx b/src/components/configuration/sections/__tests__/McpServersRenderer.test.tsx
index 4fd36638..c3f96915 100644
--- a/src/components/configuration/sections/__tests__/McpServersRenderer.test.tsx
+++ b/src/components/configuration/sections/__tests__/McpServersRenderer.test.tsx
@@ -8,6 +8,7 @@ import {
   enumerateLeafPaths,
   validateMcpCrossField,
 } from '../McpServersRenderer';
+import { applyConfigEdit, buildSavePayload } from '../../utils';
 import { createField } from '@/test/fixtures';
 
 vi.mock('@/hooks/useLocalize', () => ({
@@ -1058,3 +1059,60 @@ describe('McpServersRenderer — create then edit then rename preserves nested d
     expect(wholeHeadersWrite).toBeUndefined();
   });
 });
+
+describe('McpServersRenderer — header KV pairs never leak into the save payload (issue #56)', () => {
+  function renderWithHeaders(baseRecord: Record<string, t.ConfigValue>) {
+    const onChange = vi.fn();
+    const fields = [
+      ...fieldsForMcp(),
+      createField({ key: 'headers', type: 'record', isOptional: true }),
+    ];
+    const props: t.FieldRendererProps = {
+      fields,
+      parentValue: baseRecord,
+      parentPath: 'mcpServers',
+      getValue: (path, fallback) => (path === 'mcpServers' ? baseRecord : fallback),
+      onChange,
+      editedValues: {},
+    };
+    return { ...render(<McpServersRenderer {...props} />), onChange };
+  }
+
+  const baseRecord = {
+    srv: {
+      type: 'streamable-http',
+      url: 'https://example.com/api/mcp',
+      headers: { Authorization: 'Bearer old' },
+    },
+  };
+
+  it('serializes an edited Authorization header to a plain record in the save payload', () => {
+    const { onChange } = renderWithHeaders(baseRecord);
+
+    fireEvent.click(screen.getByText('srv'));
+    const valueInput = screen.getByLabelText('com_ui_value 1');
+    fireEvent.change(valueInput, { target: { value: 'Bearer {{API_KEY}}' } });
+    fireEvent.blur(valueInput);
+
+    const headerEdits = onChange.mock.calls.filter(([p]) => p === 'mcpServers.srv.headers');
+    expect(headerEdits.length).toBeGreaterThan(0);
+    const [path, emitted] = headerEdits[headerEdits.length - 1] as [string, t.ConfigValue];
+
+    const edited = applyConfigEdit({}, path, emitted, {}, new Set(), new Set());
+    const { saves } = buildSavePayload(new Set([path]), edited, new Set());
+    expect(saves).toEqual([
+      { fieldPath: 'mcpServers.srv.headers', value: { Authorization: 'Bearer {{API_KEY}}' } },
+    ]);
+  });
+
+  it('emits an empty record, not an empty array, when the last header row is removed', () => {
+    const { onChange } = renderWithHeaders(baseRecord);
+
+    fireEvent.click(screen.getByText('srv'));
+    fireEvent.click(screen.getByRole('button', { name: 'com_ui_delete com_ui_entry 1' }));
+
+    const headerEdits = onChange.mock.calls.filter(([p]) => p === 'mcpServers.srv.headers');
+    expect(headerEdits.length).toBeGreaterThan(0);
+    expect(headerEdits[headerEdits.length - 1][1]).toEqual({});
+  });
+});
diff --git a/src/components/configuration/utils.test.ts b/src/components/configuration/utils.test.ts
index 469644d4..6a6e6af3 100644
--- a/src/components/configuration/utils.test.ts
+++ b/src/components/configuration/utils.test.ts
@@ -9,6 +9,8 @@ import {
   mergeIndexedArrayEdits,
   buildSavePayload,
   applyConfigEdit,
+  kvPairsEditValue,
+  serializeModalValue,
 } from './utils';
 import { createField } from '@/test/fixtures';
 import { flattenObject } from '@/utils';
@@ -543,3 +545,67 @@ describe('buildSavePayload — masked secrets never reach the backend', () => {
     expect(resets).toEqual(['ocr.apiKey']);
   });
 });
+
+describe('kvPairsEditValue', () => {
+  it('passes non-empty pairs through unchanged for save-time serialization', () => {
+    const pairs: t.KeyValuePair[] = [
+      { key: 'Authorization', value: 'Bearer {{API_KEY}}', valueType: 'string' },
+    ];
+    expect(kvPairsEditValue(pairs)).toBe(pairs);
+  });
+
+  it('converts an emptied pair list to an empty record', () => {
+    expect(kvPairsEditValue([])).toEqual({});
+  });
+});
+
+describe('buildSavePayload — KV pairs serialize to records', () => {
+  it('converts header pairs edits to a plain record in the save payload', () => {
+    const edited: t.FlatConfigMap = {
+      'mcpServers.srv.headers': [
+        { key: 'Authorization', value: 'Bearer {{API_KEY}}', valueType: 'string' },
+      ],
+    };
+    const { saves } = buildSavePayload(new Set(['mcpServers.srv.headers']), edited, new Set());
+    expect(saves).toEqual([
+      { fieldPath: 'mcpServers.srv.headers', value: { Authorization: 'Bearer {{API_KEY}}' } },
+    ]);
+  });
+
+  it('converts pairs nested inside indexed array entries (azure additional params)', () => {
+    const edited: t.FlatConfigMap = {
+      'endpoints.azureOpenAI.groups.0': {
+        group: 'my-group',
+        addParams: [{ key: 'reasoning_effort', value: 'high', valueType: 'string' }],
+      },
+    };
+    const { saves } = buildSavePayload(
+      new Set(['endpoints.azureOpenAI.groups.0']),
+      edited,
+      new Set(),
+    );
+    expect(saves).toEqual([
+      {
+        fieldPath: 'endpoints.azureOpenAI.groups.0',
+        value: { group: 'my-group', addParams: { reasoning_effort: 'high' } },
+      },
+    ]);
+  });
+});
+
+describe('serializeModalValue', () => {
+  it('serializes record-control pairs to a plain record', () => {
+    const pairs = [{ key: 'Authorization', value: 'Bearer {{API_KEY}}', valueType: 'string' }];
+    expect(serializeModalValue('record', pairs)).toEqual({ Authorization: 'Bearer {{API_KEY}}' });
+  });
+
+  it('passes an untouched empty record default through unchanged', () => {
+    expect(serializeModalValue('record', {})).toEqual({});
+  });
+
+  it('leaves array-control values untouched even when elements look pair-like', () => {
+    const value = [{ key: 'id', value: 'x', enabled: true }];
+    expect(serializeModalValue('array', value)).toBe(value);
+    expect(serializeModalValue('array-object', value)).toBe(value);
+  });
+});
diff --git a/src/components/configuration/utils.ts b/src/components/configuration/utils.ts
index d858cecc..3ab8e278 100644
--- a/src/components/configuration/utils.ts
+++ b/src/components/configuration/utils.ts
@@ -1,5 +1,10 @@
 import type * as t from '@/types';
-import { deepSerializeKVPairs, secretPathForPreviewPath, stripSecretPreviewValues } from '@/utils';
+import {
+  deepSerializeKVPairs,
+  secretPathForPreviewPath,
+  stripSecretPreviewValues,
+  serializeKVPairs,
+} from '@/utils';
 
 const INDEXED_ARRAY_PATH_RE = /^(.+)\.(\d+)$/;
 
@@ -34,6 +39,27 @@ export function inferKVType(v: t.ConfigValue): t.KVValueType {
   return 'string';
 }
 
+/**
+ * Wraps a KeyValueField edit for storage in edit state. In-progress rows stay
+ * as raw pairs so blank keys survive re-renders until save-time serialization,
+ * but an emptied list must become an empty record immediately: a bare `[]`
+ * cannot be recognized as KV pairs by `serializeKVPairs` and would reach the
+ * backend as an array where the schema expects an object.
+ */
+export function kvPairsEditValue(pairs: t.KeyValuePair[]): t.ConfigValue {
+  return pairs.length === 0 ? {} : pairs;
+}
+
+/**
+ * Serializes a profile modal value for save. Only record controls edit via
+ * KeyValueField pairs; every other control type must pass through untouched
+ * so array values whose elements merely look pair-like (objects carrying
+ * `key` and `value` properties) are never collapsed into records.
+ */
+export function serializeModalValue(controlType: t.ControlType, value: t.ConfigValue): t.ConfigValue {
+  return controlType === 'record' ? serializeKVPairs(value) : value;
+}
+
 export function toKVPair(k: string, v: t.ConfigValue): t.KeyValuePair {
   const valueType = inferKVType(v);
   if (valueType === 'json') return { key: k, value: JSON.stringify(v, null, 2), valueType };