diff --git a/src/core/webview/ClineProvider.ts b/src/core/webview/ClineProvider.ts
index f4c26c3dfc..432ac6420b 100644
--- a/src/core/webview/ClineProvider.ts
+++ b/src/core/webview/ClineProvider.ts
@@ -49,6 +49,7 @@ import { ACTION_NAMES } from "../CodeActionProvider"
 import { Cline, ClineOptions } from "../Cline"
 import { getNonce } from "./getNonce"
 import { getUri } from "./getUri"
+import { getSystemPromptFilePath } from "../prompts/sections/custom-system-prompt"
 import { telemetryService } from "../../services/telemetry/TelemetryService"
 import { getWorkspacePath } from "../../utils/path"
 import { webviewMessageHandler } from "./webviewMessageHandler"
@@ -1161,6 +1162,14 @@ export class ClineProvider extends EventEmitter<ClineProviderEvents> implements
 		this.postMessageToWebview({ type: "state", state })
 	}
 
+	/**
+	 * Checks if there is a file-based system prompt override for the given mode
+	 */
+	async hasFileBasedSystemPromptOverride(mode: Mode): Promise<boolean> {
+		const promptFilePath = getSystemPromptFilePath(this.cwd, mode)
+		return await fileExistsAtPath(promptFilePath)
+	}
+
 	async getStateToPostToWebview() {
 		const {
 			apiConfiguration,
@@ -1224,6 +1233,10 @@ export class ClineProvider extends EventEmitter<ClineProviderEvents> implements
 		const allowedCommands = vscode.workspace.getConfiguration("roo-cline").get<string[]>("allowedCommands") || []
 		const cwd = this.cwd
 
+		// Check if there's a system prompt override for the current mode
+		const currentMode = mode ?? defaultModeSlug
+		const hasSystemPromptOverride = await this.hasFileBasedSystemPromptOverride(currentMode)
+
 		return {
 			version: this.context.extension?.packageJSON?.version ?? "",
 			apiConfiguration,
@@ -1296,6 +1309,7 @@ export class ClineProvider extends EventEmitter<ClineProviderEvents> implements
 			renderContext: this.renderContext,
 			maxReadFileLine: maxReadFileLine ?? 500,
 			settingsImportedAt: this.settingsImportedAt,
+			hasSystemPromptOverride,
 		}
 	}
 
diff --git a/src/shared/WebviewMessage.ts b/src/shared/WebviewMessage.ts
index f1ab993679..83725bc5c3 100644
--- a/src/shared/WebviewMessage.ts
+++ b/src/shared/WebviewMessage.ts
@@ -150,6 +150,7 @@ export interface WebviewMessage {
 	source?: "global" | "project"
 	requestId?: string
 	ids?: string[]
+	hasSystemPromptOverride?: boolean
 }
 
 export const checkoutDiffPayloadSchema = z.object({
diff --git a/webview-ui/src/components/chat/ChatView.tsx b/webview-ui/src/components/chat/ChatView.tsx
index 23072e7b9c..7b84b81ab9 100644
--- a/webview-ui/src/components/chat/ChatView.tsx
+++ b/webview-ui/src/components/chat/ChatView.tsx
@@ -27,6 +27,7 @@ import ChatRow from "./ChatRow"
 import ChatTextArea from "./ChatTextArea"
 import TaskHeader from "./TaskHeader"
 import AutoApproveMenu from "./AutoApproveMenu"
+import SystemPromptWarning from "./SystemPromptWarning"
 import { AudioType } from "@roo/shared/WebviewMessage"
 import { validateCommand } from "@src/utils/command-validation"
 import { getAllModes } from "@roo/shared/modes"
@@ -77,6 +78,7 @@ const ChatViewComponent: React.ForwardRefRenderFunction<ChatViewRef, ChatViewPro
 		alwaysAllowSubtasks,
 		customModes,
 		telemetrySetting,
+		hasSystemPromptOverride,
 	} = useExtensionState()
 
 	//const task = messages.length > 0 ? (messages[0].say === "task" ? messages[0] : undefined) : undefined) : undefined
@@ -1205,6 +1207,13 @@ const ChatViewComponent: React.ForwardRefRenderFunction<ChatViewRef, ChatViewPro
 						onClose={handleTaskCloseButtonClick}
 					/>
 
+					{/* System prompt override warning */}
+					{hasSystemPromptOverride && (
+						<div className="px-3">
+							<SystemPromptWarning />
+						</div>
+					)}
+
 					{/* Checkpoint warning message */}
 					{showCheckpointWarning && (
 						<div className="px-3">
diff --git a/webview-ui/src/components/chat/SystemPromptWarning.tsx b/webview-ui/src/components/chat/SystemPromptWarning.tsx
new file mode 100644
index 0000000000..0ed7a72733
--- /dev/null
+++ b/webview-ui/src/components/chat/SystemPromptWarning.tsx
@@ -0,0 +1,17 @@
+import React from "react"
+import { useAppTranslation } from "@/i18n/TranslationContext"
+
+export const SystemPromptWarning: React.FC = () => {
+	const { t } = useAppTranslation()
+
+	return (
+		<div className="flex items-center px-4 py-2 mb-2 text-sm rounded bg-vscode-editorWarning-foreground text-vscode-editor-background">
+			<div className="flex items-center justify-center w-5 h-5 mr-2">
+				<span className="codicon codicon-warning" />
+			</div>
+			<span>{t("chat:systemPromptWarning")}</span>
+		</div>
+	)
+}
+
+export default SystemPromptWarning
diff --git a/webview-ui/src/context/ExtensionStateContext.tsx b/webview-ui/src/context/ExtensionStateContext.tsx
index 26f43db81a..90629edfb1 100644
--- a/webview-ui/src/context/ExtensionStateContext.tsx
+++ b/webview-ui/src/context/ExtensionStateContext.tsx
@@ -17,6 +17,7 @@ export interface ExtensionStateContextType extends ExtensionState {
 	showWelcome: boolean
 	theme: any
 	mcpServers: McpServer[]
+	hasSystemPromptOverride?: boolean
 	currentCheckpoint?: string
 	filePaths: string[]
 	openedTabs: Array<{ label: string; isActive: boolean; path?: string }>
diff --git a/webview-ui/src/i18n/locales/ca/chat.json b/webview-ui/src/i18n/locales/ca/chat.json
index 702a86fc1f..fcad714a7e 100644
--- a/webview-ui/src/i18n/locales/ca/chat.json
+++ b/webview-ui/src/i18n/locales/ca/chat.json
@@ -211,5 +211,6 @@
 			"scrollUp": "Desplaçar amunt",
 			"close": "Tancar navegador"
 		}
-	}
+	},
+	"systemPromptWarning": "ADVERTÈNCIA: S'ha activat una substitució personalitzada d'instruccions del sistema. Això pot trencar greument la funcionalitat i causar un comportament impredictible."
 }
diff --git a/webview-ui/src/i18n/locales/de/chat.json b/webview-ui/src/i18n/locales/de/chat.json
index e416423f98..ef92900bac 100644
--- a/webview-ui/src/i18n/locales/de/chat.json
+++ b/webview-ui/src/i18n/locales/de/chat.json
@@ -211,5 +211,6 @@
 			"scrollUp": "Nach oben scrollen",
 			"close": "Browser schließen"
 		}
-	}
+	},
+	"systemPromptWarning": "WARNUNG: Benutzerdefinierte Systemaufforderung aktiv. Dies kann die Funktionalität erheblich beeinträchtigen und zu unvorhersehbarem Verhalten führen."
 }
diff --git a/webview-ui/src/i18n/locales/en/chat.json b/webview-ui/src/i18n/locales/en/chat.json
index 6f4a0a1e54..1c077b1761 100644
--- a/webview-ui/src/i18n/locales/en/chat.json
+++ b/webview-ui/src/i18n/locales/en/chat.json
@@ -211,5 +211,6 @@
 			"scrollUp": "Scroll up",
 			"close": "Close browser"
 		}
-	}
+	},
+	"systemPromptWarning": "WARNING: Custom system prompt override active. This can severely break functionality and cause unpredictable behavior."
 }
diff --git a/webview-ui/src/i18n/locales/es/chat.json b/webview-ui/src/i18n/locales/es/chat.json
index 9743ed85f5..ac46118723 100644
--- a/webview-ui/src/i18n/locales/es/chat.json
+++ b/webview-ui/src/i18n/locales/es/chat.json
@@ -211,5 +211,6 @@
 			"scrollUp": "Desplazar hacia arriba",
 			"close": "Cerrar navegador"
 		}
-	}
+	},
+	"systemPromptWarning": "ADVERTENCIA: Anulación de instrucciones del sistema personalizada activa. Esto puede romper gravemente la funcionalidad y causar un comportamiento impredecible."
 }
diff --git a/webview-ui/src/i18n/locales/fr/chat.json b/webview-ui/src/i18n/locales/fr/chat.json
index 0025d82889..f5b6a6135e 100644
--- a/webview-ui/src/i18n/locales/fr/chat.json
+++ b/webview-ui/src/i18n/locales/fr/chat.json
@@ -211,5 +211,6 @@
 			"scrollUp": "Défiler vers le haut",
 			"close": "Fermer le navigateur"
 		}
-	}
+	},
+	"systemPromptWarning": "AVERTISSEMENT : Remplacement d'instructions système personnalisées actif. Cela peut gravement perturber la fonctionnalité et provoquer un comportement imprévisible."
 }
diff --git a/webview-ui/src/i18n/locales/hi/chat.json b/webview-ui/src/i18n/locales/hi/chat.json
index f4391e624f..91491cf3e6 100644
--- a/webview-ui/src/i18n/locales/hi/chat.json
+++ b/webview-ui/src/i18n/locales/hi/chat.json
@@ -211,5 +211,6 @@
 			"scrollUp": "ऊपर स्क्रॉल करें",
 			"close": "ब्राउज़र बंद करें"
 		}
-	}
+	},
+	"systemPromptWarning": "चेतावनी: कस्टम सिस्टम प्रॉम्प्ट ओवरराइड सक्रिय है। यह कार्यक्षमता को गंभीर रूप से बाधित कर सकता है और अनियमित व्यवहार का कारण बन सकता है।"
 }
diff --git a/webview-ui/src/i18n/locales/it/chat.json b/webview-ui/src/i18n/locales/it/chat.json
index 62921786d1..d54dd9a95c 100644
--- a/webview-ui/src/i18n/locales/it/chat.json
+++ b/webview-ui/src/i18n/locales/it/chat.json
@@ -211,5 +211,6 @@
 			"scrollUp": "Scorri verso l'alto",
 			"close": "Chiudi browser"
 		}
-	}
+	},
+	"systemPromptWarning": "ATTENZIONE: Sovrascrittura personalizzata delle istruzioni di sistema attiva. Questo può compromettere gravemente le funzionalità e causare comportamenti imprevedibili."
 }
diff --git a/webview-ui/src/i18n/locales/ja/chat.json b/webview-ui/src/i18n/locales/ja/chat.json
index 4d0b2d6413..31094a763c 100644
--- a/webview-ui/src/i18n/locales/ja/chat.json
+++ b/webview-ui/src/i18n/locales/ja/chat.json
@@ -211,5 +211,6 @@
 			"scrollUp": "上にスクロール",
 			"close": "ブラウザを閉じる"
 		}
-	}
+	},
+	"systemPromptWarning": "警告：カスタムシステムプロンプトの上書きが有効です。これにより機能が深刻に損なわれ、予測不可能な動作が発生する可能性があります。"
 }
diff --git a/webview-ui/src/i18n/locales/ko/chat.json b/webview-ui/src/i18n/locales/ko/chat.json
index 40c3c580d7..938bdca76b 100644
--- a/webview-ui/src/i18n/locales/ko/chat.json
+++ b/webview-ui/src/i18n/locales/ko/chat.json
@@ -211,5 +211,6 @@
 			"scrollUp": "위로 스크롤",
 			"close": "브라우저 닫기"
 		}
-	}
+	},
+	"systemPromptWarning": "경고: 사용자 정의 시스템 프롬프트 재정의가 활성화되었습니다. 이로 인해 기능이 심각하게 손상되고 예측할 수 없는 동작이 발생할 수 있습니다."
 }
diff --git a/webview-ui/src/i18n/locales/pl/chat.json b/webview-ui/src/i18n/locales/pl/chat.json
index db17efd24f..10884b102a 100644
--- a/webview-ui/src/i18n/locales/pl/chat.json
+++ b/webview-ui/src/i18n/locales/pl/chat.json
@@ -211,5 +211,6 @@
 			"scrollUp": "Przewiń w górę",
 			"close": "Zamknij przeglądarkę"
 		}
-	}
+	},
+	"systemPromptWarning": "OSTRZEŻENIE: Aktywne niestandardowe zastąpienie instrukcji systemowych. Może to poważnie zakłócić funkcjonalność i powodować nieprzewidywalne zachowanie."
 }
diff --git a/webview-ui/src/i18n/locales/pt-BR/chat.json b/webview-ui/src/i18n/locales/pt-BR/chat.json
index 8d6c420236..fe6ef1bdef 100644
--- a/webview-ui/src/i18n/locales/pt-BR/chat.json
+++ b/webview-ui/src/i18n/locales/pt-BR/chat.json
@@ -211,5 +211,6 @@
 			"scrollUp": "Rolar para cima",
 			"close": "Fechar navegador"
 		}
-	}
+	},
+	"systemPromptWarning": "AVISO: Substituição personalizada de instrução do sistema ativa. Isso pode comprometer gravemente a funcionalidade e causar comportamento imprevisível."
 }
diff --git a/webview-ui/src/i18n/locales/tr/chat.json b/webview-ui/src/i18n/locales/tr/chat.json
index 1f46537a31..34c5fd2911 100644
--- a/webview-ui/src/i18n/locales/tr/chat.json
+++ b/webview-ui/src/i18n/locales/tr/chat.json
@@ -211,5 +211,6 @@
 			"scrollUp": "Yukarı kaydır",
 			"close": "Tarayıcıyı kapat"
 		}
-	}
+	},
+	"systemPromptWarning": "UYARI: Özel sistem komut geçersiz kılma aktif. Bu işlevselliği ciddi şekilde bozabilir ve öngörülemeyen davranışlara neden olabilir."
 }
diff --git a/webview-ui/src/i18n/locales/vi/chat.json b/webview-ui/src/i18n/locales/vi/chat.json
index 08e5ef4fe8..3fe66b54ba 100644
--- a/webview-ui/src/i18n/locales/vi/chat.json
+++ b/webview-ui/src/i18n/locales/vi/chat.json
@@ -211,5 +211,6 @@
 			"scrollUp": "Cuộn lên",
 			"close": "Đóng trình duyệt"
 		}
-	}
+	},
+	"systemPromptWarning": "CẢNH BÁO: Đã kích hoạt ghi đè lệnh nhắc hệ thống tùy chỉnh. Điều này có thể phá vỡ nghiêm trọng chức năng và gây ra hành vi không thể dự đoán."
 }
diff --git a/webview-ui/src/i18n/locales/zh-CN/chat.json b/webview-ui/src/i18n/locales/zh-CN/chat.json
index 569c80be9f..3772e10884 100644
--- a/webview-ui/src/i18n/locales/zh-CN/chat.json
+++ b/webview-ui/src/i18n/locales/zh-CN/chat.json
@@ -211,5 +211,6 @@
 			"scrollUp": "向上滚动",
 			"close": "关闭浏览器"
 		}
-	}
+	},
+	"systemPromptWarning": "警告：自定义系统提示词覆盖已激活。这可能严重破坏功能并导致不可预测的行为。"
 }
diff --git a/webview-ui/src/i18n/locales/zh-TW/chat.json b/webview-ui/src/i18n/locales/zh-TW/chat.json
index e7d239e930..d9c745ebf3 100644
--- a/webview-ui/src/i18n/locales/zh-TW/chat.json
+++ b/webview-ui/src/i18n/locales/zh-TW/chat.json
@@ -211,5 +211,6 @@
 			"scrollUp": "向上捲動",
 			"close": "關閉瀏覽器"
 		}
-	}
+	},
+	"systemPromptWarning": "警告：自訂系統提示詞覆蓋已啟用。這可能嚴重破壞功能並導致不可預測的行為。"
 }
diff --git a/webview-ui/src/index.css b/webview-ui/src/index.css
index 21421c66ac..efc7e8c11e 100644
--- a/webview-ui/src/index.css
+++ b/webview-ui/src/index.css
@@ -68,6 +68,9 @@
 
 	--color-vscode-editorGroup-border: var(--vscode-editorGroup-border);
 
+	--color-vscode-editorWarning-foreground: var(--vscode-editorWarning-foreground);
+	--color-vscode-editorWarning-background: var(--vscode-editorWarning-background);
+
 	--color-vscode-button-foreground: var(--vscode-button-foreground);
 	--color-vscode-button-background: var(--vscode-button-background);
 	--color-vscode-button-secondaryForeground: var(--vscode-button-secondaryForeground);