diff --git a/frontend/src/lib/components/projects/ProjectModal.svelte b/frontend/src/lib/components/projects/ProjectModal.svelte
index 70b1e54..ed25e6b 100644
--- a/frontend/src/lib/components/projects/ProjectModal.svelte
+++ b/frontend/src/lib/components/projects/ProjectModal.svelte
@@ -5,6 +5,7 @@
 	import { projectsState, toastState } from '$lib/stores';
 	import type { Project } from '$lib/stores/projects.svelte.js';
 	import { addProjectLink, deleteProjectLink, getProjectLinks, type ProjectLink } from '$lib/storage/projects.js';
+	import { ConfirmDialog } from '$lib/components/shared';
 
 	interface Props {
 		isOpen: boolean;
@@ -26,6 +27,7 @@
 	let newLinkDescription = $state('');
 	let isLoading = $state(false);
 	let activeTab = $state<'settings' | 'instructions' | 'links'>('settings');
+	let showDeleteConfirm = $state(false);
 
 	// Predefined colors for quick selection
 	const presetColors = [
@@ -121,13 +123,14 @@
 		}
 	}
 
-	async function handleDelete() {
+	function handleDeleteClick() {
 		if (!projectId) return;
+		showDeleteConfirm = true;
+	}
 
-		if (!confirm('Delete this project? Conversations will be unlinked but not deleted.')) {
-			return;
-		}
-
+	async function handleDeleteConfirm() {
+		if (!projectId) return;
+		showDeleteConfirm = false;
 		isLoading = true;
 
 		try {
@@ -429,7 +432,7 @@
 					{#if projectId}
 						<button
 							type="button"
-							onclick={handleDelete}
+							onclick={handleDeleteClick}
 							disabled={isLoading}
 							class="rounded-lg px-4 py-2 text-sm font-medium text-red-500 transition-colors hover:bg-red-900/30 disabled:opacity-50"
 						>
@@ -458,3 +461,13 @@
 		</div>
 	</div>
 {/if}
+
+<ConfirmDialog
+	isOpen={showDeleteConfirm}
+	title="Delete Project"
+	message="Delete this project? Conversations will be unlinked but not deleted."
+	confirmText="Delete"
+	variant="danger"
+	onConfirm={handleDeleteConfirm}
+	onCancel={() => (showDeleteConfirm = false)}
+/>
diff --git a/frontend/src/lib/components/settings/KnowledgeTab.svelte b/frontend/src/lib/components/settings/KnowledgeTab.svelte
index 151ae2b..f11beb1 100644
--- a/frontend/src/lib/components/settings/KnowledgeTab.svelte
+++ b/frontend/src/lib/components/settings/KnowledgeTab.svelte
@@ -14,6 +14,7 @@
 	} from '$lib/memory';
 	import type { StoredDocument } from '$lib/storage/db';
 	import { toastState, modelsState } from '$lib/stores';
+	import { ConfirmDialog } from '$lib/components/shared';
 
 	let documents = $state<StoredDocument[]>([]);
 	let stats = $state({ documentCount: 0, chunkCount: 0, totalTokens: 0 });
@@ -22,6 +23,7 @@
 	let uploadProgress = $state({ current: 0, total: 0 });
 	let selectedModel = $state(DEFAULT_EMBEDDING_MODEL);
 	let dragOver = $state(false);
+	let deleteConfirm = $state<{ show: boolean; doc: StoredDocument | null }>({ show: false, doc: null });
 
 	let fileInput: HTMLInputElement;
 
@@ -90,10 +92,14 @@
 		uploadProgress = { current: 0, total: 0 };
 	}
 
-	async function handleDelete(doc: StoredDocument) {
-		if (!confirm(`Delete "${doc.name}"? This cannot be undone.`)) {
-			return;
-		}
+	function handleDeleteClick(doc: StoredDocument) {
+		deleteConfirm = { show: true, doc };
+	}
+
+	async function confirmDelete() {
+		if (!deleteConfirm.doc) return;
+		const doc = deleteConfirm.doc;
+		deleteConfirm = { show: false, doc: null };
 
 		try {
 			await deleteDocument(doc.id);
@@ -232,7 +238,7 @@
 
 						<button
 							type="button"
-							onclick={() => handleDelete(doc)}
+							onclick={() => handleDeleteClick(doc)}
 							class="rounded p-2 text-theme-muted transition-colors hover:bg-red-900/30 hover:text-red-400"
 							aria-label="Delete document"
 						>
@@ -273,3 +279,13 @@
 		{/if}
 	</section>
 </div>
+
+<ConfirmDialog
+	isOpen={deleteConfirm.show}
+	title="Delete Document"
+	message={`Delete "${deleteConfirm.doc?.name}"? This cannot be undone.`}
+	confirmText="Delete"
+	variant="danger"
+	onConfirm={confirmDelete}
+	onCancel={() => (deleteConfirm = { show: false, doc: null })}
+/>
diff --git a/frontend/src/lib/components/settings/PromptsTab.svelte b/frontend/src/lib/components/settings/PromptsTab.svelte
index 492c624..0ba5be4 100644
--- a/frontend/src/lib/components/settings/PromptsTab.svelte
+++ b/frontend/src/lib/components/settings/PromptsTab.svelte
@@ -10,9 +10,11 @@
 		type PromptTemplate,
 		type PromptCategory
 	} from '$lib/prompts/templates';
+	import { ConfirmDialog } from '$lib/components/shared';
 
 	type Tab = 'my-prompts' | 'browse-templates';
 	let activeTab = $state<Tab>('my-prompts');
+	let deleteConfirm = $state<{ show: boolean; prompt: Prompt | null }>({ show: false, prompt: null });
 
 	let showEditor = $state(false);
 	let editingPrompt = $state<Prompt | null>(null);
@@ -106,10 +108,14 @@
 		}
 	}
 
-	async function handleDelete(prompt: Prompt): Promise<void> {
-		if (confirm(`Delete "${prompt.name}"? This cannot be undone.`)) {
-			await promptsState.remove(prompt.id);
-		}
+	function handleDeleteClick(prompt: Prompt): void {
+		deleteConfirm = { show: true, prompt };
+	}
+
+	async function confirmDelete(): Promise<void> {
+		if (!deleteConfirm.prompt) return;
+		await promptsState.remove(deleteConfirm.prompt.id);
+		deleteConfirm = { show: false, prompt: null };
 	}
 
 	async function handleSetDefault(prompt: Prompt): Promise<void> {
@@ -286,7 +292,7 @@
 										<path stroke-linecap="round" stroke-linejoin="round" d="M11 5H6a2 2 0 00-2 2v11a2 2 0 002 2h11a2 2 0 002-2v-5m-1.414-9.414a2 2 0 112.828 2.828L11.828 15H9v-2.828l8.586-8.586z" />
 									</svg>
 								</button>
-								<button type="button" onclick={() => handleDelete(prompt)} class="rounded p-1.5 text-theme-muted hover:bg-red-900/30 hover:text-red-400" title="Delete">
+								<button type="button" onclick={() => handleDeleteClick(prompt)} class="rounded p-1.5 text-theme-muted hover:bg-red-900/30 hover:text-red-400" title="Delete">
 									<svg xmlns="http://www.w3.org/2000/svg" class="h-4 w-4" fill="none" viewBox="0 0 24 24" stroke="currentColor" stroke-width="2">
 										<path stroke-linecap="round" stroke-linejoin="round" d="M19 7l-.867 12.142A2 2 0 0116.138 21H7.862a2 2 0 01-1.995-1.858L5 7m5 4v6m4-6v6m1-10V4a1 1 0 00-1-1h-4a1 1 0 00-1 1v3M4 7h16" />
 									</svg>
@@ -444,3 +450,13 @@
 		</div>
 	</div>
 {/if}
+
+<ConfirmDialog
+	isOpen={deleteConfirm.show}
+	title="Delete Prompt"
+	message={`Delete "${deleteConfirm.prompt?.name}"? This cannot be undone.`}
+	confirmText="Delete"
+	variant="danger"
+	onConfirm={confirmDelete}
+	onCancel={() => (deleteConfirm = { show: false, prompt: null })}
+/>
diff --git a/frontend/src/lib/components/settings/ToolsTab.svelte b/frontend/src/lib/components/settings/ToolsTab.svelte
index f5dffbb..5a44e44 100644
--- a/frontend/src/lib/components/settings/ToolsTab.svelte
+++ b/frontend/src/lib/components/settings/ToolsTab.svelte
@@ -5,11 +5,13 @@
 	import { toolsState } from '$lib/stores';
 	import type { ToolDefinition, CustomTool } from '$lib/tools';
 	import { ToolEditor } from '$lib/components/tools';
+	import { ConfirmDialog } from '$lib/components/shared';
 
 	let showEditor = $state(false);
 	let editingTool = $state<CustomTool | null>(null);
 	let searchQuery = $state('');
 	let expandedDescriptions = $state<Set<string>>(new Set());
+	let deleteConfirm = $state<{ show: boolean; tool: CustomTool | null }>({ show: false, tool: null });
 
 	function openCreateEditor(): void {
 		editingTool = null;
@@ -32,9 +34,14 @@
 	}
 
 	function handleDeleteTool(tool: CustomTool): void {
-		if (confirm(`Delete "${tool.name}"? This cannot be undone.`)) {
-			toolsState.removeCustomTool(tool.id);
+		deleteConfirm = { show: true, tool };
+	}
+
+	function confirmDeleteTool(): void {
+		if (deleteConfirm.tool) {
+			toolsState.removeCustomTool(deleteConfirm.tool.id);
 		}
+		deleteConfirm = { show: false, tool: null };
 	}
 
 	const allTools = $derived(toolsState.getAllToolsWithState());
@@ -509,3 +516,13 @@
 	onClose={() => { showEditor = false; editingTool = null; }}
 	onSave={handleSaveTool}
 />
+
+<ConfirmDialog
+	isOpen={deleteConfirm.show}
+	title="Delete Tool"
+	message={`Delete "${deleteConfirm.tool?.name}"? This cannot be undone.`}
+	confirmText="Delete"
+	variant="danger"
+	onConfirm={confirmDeleteTool}
+	onCancel={() => (deleteConfirm = { show: false, tool: null })}
+/>
diff --git a/frontend/src/lib/storage/projects.ts b/frontend/src/lib/storage/projects.ts
index 32a6868..e44fbd8 100644
--- a/frontend/src/lib/storage/projects.ts
+++ b/frontend/src/lib/storage/projects.ts
@@ -175,7 +175,7 @@ export async function updateProject(
  */
 export async function deleteProject(id: string): Promise<StorageResult<void>> {
 	return withErrorHandling(async () => {
-		await db.transaction('rw', [db.projects, db.projectLinks, db.conversations, db.documents, db.chatChunks], async () => {
+		await db.transaction('rw', [db.projects, db.projectLinks, db.conversations, db.documents, db.chunks, db.chatChunks], async () => {
 			// Unlink all conversations from this project
 			const conversations = await db.conversations.where('projectId').equals(id).toArray();
 			for (const conv of conversations) {
diff --git a/frontend/src/routes/projects/[id]/+page.svelte b/frontend/src/routes/projects/[id]/+page.svelte
index e0f0e72..61446c3 100644
--- a/frontend/src/routes/projects/[id]/+page.svelte
+++ b/frontend/src/routes/projects/[id]/+page.svelte
@@ -20,6 +20,7 @@
 	import type { StoredDocument } from '$lib/storage/db';
 	import ProjectModal from '$lib/components/projects/ProjectModal.svelte';
 	import { searchProjectChatHistory, type ChatSearchResult } from '$lib/services/chat-indexer.js';
+	import { ConfirmDialog } from '$lib/components/shared';
 
 	// Get project ID from URL
 	const projectId = $derived($page.params.id);
@@ -50,6 +51,7 @@
 	let isSearching = $state(false);
 	let searchResults = $state<ChatSearchResult[]>([]);
 	let searchDebounceTimer: ReturnType<typeof setTimeout> | null = null;
+	let deleteDocConfirm = $state<{ show: boolean; doc: StoredDocument | null }>({ show: false, doc: null });
 
 	// Map of conversationId -> best matching snippet from search
 	const searchSnippetMap = $derived.by(() => {
@@ -323,8 +325,14 @@
 		await loadProjectData();
 	}
 
-	async function handleDeleteDocument(doc: StoredDocument) {
-		if (!confirm(`Delete "${doc.name}"? This cannot be undone.`)) return;
+	function handleDeleteDocumentClick(doc: StoredDocument) {
+		deleteDocConfirm = { show: true, doc };
+	}
+
+	async function confirmDeleteDocument() {
+		if (!deleteDocConfirm.doc) return;
+		const doc = deleteDocConfirm.doc;
+		deleteDocConfirm = { show: false, doc: null };
 
 		try {
 			await deleteDocument(doc.id);
@@ -632,7 +640,7 @@
 									</div>
 									<button
 										type="button"
-										onclick={() => handleDeleteDocument(doc)}
+										onclick={() => handleDeleteDocumentClick(doc)}
 										class="rounded p-1.5 text-theme-muted transition-colors hover:bg-red-900/30 hover:text-red-400"
 									>
 										<svg xmlns="http://www.w3.org/2000/svg" class="h-4 w-4" fill="none" viewBox="0 0 24 24" stroke="currentColor" stroke-width="2">
@@ -705,3 +713,14 @@
 	{projectId}
 	onUpdate={() => loadProjectData()}
 />
+
+<!-- Delete Document Confirm -->
+<ConfirmDialog
+	isOpen={deleteDocConfirm.show}
+	title="Delete Document"
+	message={`Delete "${deleteDocConfirm.doc?.name}"? This cannot be undone.`}
+	confirmText="Delete"
+	variant="danger"
+	onConfirm={confirmDeleteDocument}
+	onCancel={() => (deleteDocConfirm = { show: false, doc: null })}
+/>