diff --git a/apps/dokploy/components/dashboard/application/patches/create-file-dialog.tsx b/apps/dokploy/components/dashboard/application/patches/create-file-dialog.tsx
new file mode 100644
index 000000000..5f6f88e36
--- /dev/null
+++ b/apps/dokploy/components/dashboard/application/patches/create-file-dialog.tsx
@@ -0,0 +1,107 @@
+import { FilePlus } from "lucide-react";
+import { useState } from "react";
+import { CodeEditor } from "@/components/shared/code-editor";
+import { Button } from "@/components/ui/button";
+import {
+	Dialog,
+	DialogClose,
+	DialogContent,
+	DialogDescription,
+	DialogFooter,
+	DialogHeader,
+	DialogTitle,
+	DialogTrigger,
+} from "@/components/ui/dialog";
+import { Input } from "@/components/ui/input";
+import { Label } from "@/components/ui/label";
+
+interface Props {
+	folderPath: string;
+	onCreate: (filename: string, content: string) => void;
+	onOpenChange: (open: boolean) => void;
+	alwaysVisible?: boolean;
+}
+
+export const CreateFileDialog = ({
+	folderPath,
+	onCreate,
+	onOpenChange,
+	alwaysVisible = false,
+}: Props) => {
+	const [filename, setFilename] = useState("");
+	const [content, setContent] = useState("");
+
+	const handleCreate = () => {
+		if (!filename.trim()) return;
+		onCreate(filename.trim(), content);
+		setFilename("");
+		setContent("");
+		onOpenChange(false);
+	};
+
+	return (
+		<Dialog>
+			<DialogTrigger asChild>
+				<Button
+					variant="ghost"
+					size="icon"
+					type="button"
+					className={`h-6 w-6 ${alwaysVisible ? "" : "opacity-0 group-hover:opacity-100"}`}
+					title="Create file"
+				>
+					<FilePlus className="h-3 w-3" />
+				</Button>
+			</DialogTrigger>
+			<DialogContent className="sm:max-w-2xl">
+				<form
+					onSubmit={(e) => {
+						e.preventDefault();
+						handleCreate();
+					}}
+				>
+					<DialogHeader>
+						<DialogTitle>Create file</DialogTitle>
+						<DialogDescription>
+							{folderPath ? `New file in ${folderPath}/` : "New file in root"}
+						</DialogDescription>
+					</DialogHeader>
+					<div className="space-y-4 py-4">
+						<div className="space-y-2">
+							<Label htmlFor="filename">Filename</Label>
+							<Input
+								id="filename"
+								placeholder="e.g. .env.example"
+								value={filename}
+								onChange={(e) => setFilename(e.target.value)}
+							/>
+						</div>
+						<div className="space-y-2">
+							<Label>Content</Label>
+							<div className="h-[200px] rounded-md border">
+								<CodeEditor
+									value={content}
+									onChange={(v) => setContent(v ?? "")}
+									className="h-full"
+									wrapperClassName="h-[200px]"
+									lineWrapping
+								/>
+							</div>
+						</div>
+					</div>
+					<DialogFooter>
+						<DialogClose asChild>
+							<Button variant="outline" type="button">
+								Cancel
+							</Button>
+						</DialogClose>
+						<DialogClose asChild>
+							<Button type="submit" disabled={!filename.trim()}>
+								Create
+							</Button>
+						</DialogClose>
+					</DialogFooter>
+				</form>
+			</DialogContent>
+		</Dialog>
+	);
+};
diff --git a/apps/dokploy/components/dashboard/application/patches/patch-editor.tsx b/apps/dokploy/components/dashboard/application/patches/patch-editor.tsx
index 9f0608260..ba38e29a6 100644
--- a/apps/dokploy/components/dashboard/application/patches/patch-editor.tsx
+++ b/apps/dokploy/components/dashboard/application/patches/patch-editor.tsx
@@ -5,8 +5,9 @@ import {
 	Folder,
 	Loader2,
 	Save,
+	Trash2,
 } from "lucide-react";
-import { useCallback, useState } from "react";
+import { useCallback, useEffect, useState } from "react";
 import { toast } from "sonner";
 import { CodeEditor } from "@/components/shared/code-editor";
 import { Button } from "@/components/ui/button";
@@ -19,6 +20,7 @@ import {
 } from "@/components/ui/card";
 import { ScrollArea } from "@/components/ui/scroll-area";
 import { api } from "@/utils/api";
+import { CreateFileDialog } from "./create-file-dialog";
 
 interface Props {
 	id: string;
@@ -37,20 +39,31 @@ type DirectoryEntry = {
 export const PatchEditor = ({ id, type, repoPath, onClose }: Props) => {
 	const [selectedFile, setSelectedFile] = useState<string | null>(null);
 	const [fileContent, setFileContent] = useState<string>("");
-	const [originalContent, setOriginalContent] = useState<string>("");
+	const [createFolderPath, setCreateFolderPath] = useState<string | null>(null);
 	const [expandedFolders, setExpandedFolders] = useState<Set<string>>(
 		new Set(),
 	);
 
+	const utils = api.useUtils();
 	const { data: directories, isLoading: isDirLoading } =
 		api.patch.readRepoDirectories.useQuery(
 			{ id: id, type, repoPath },
 			{ enabled: !!repoPath },
 		);
 
+	const { data: patches } = api.patch.byEntityId.useQuery(
+		{ id, type },
+		{ enabled: !!id },
+	);
+
 	const { mutateAsync: saveAsPatch, isLoading: isSavingPatch } =
 		api.patch.saveFileAsPatch.useMutation();
 
+	const { mutateAsync: markForDeletion, isLoading: isMarkingDeletion } =
+		api.patch.markFileForDeletion.useMutation();
+
+	const updatePatch = api.patch.update.useMutation();
+
 	const { data: fileData, isFetching: isFileLoading } =
 		api.patch.readRepoFile.useQuery(
 			{
@@ -63,6 +76,12 @@ export const PatchEditor = ({ id, type, repoPath, onClose }: Props) => {
 			},
 		);
 
+	useEffect(() => {
+		if (fileData !== undefined) {
+			setFileContent(fileData);
+		}
+	}, [fileData]);
+
 	const handleFileSelect = (filePath: string) => {
 		setSelectedFile(filePath);
 	};
@@ -86,16 +105,72 @@ export const PatchEditor = ({ id, type, repoPath, onClose }: Props) => {
 			type,
 			filePath: selectedFile,
 			content: fileContent,
+			patchType: "update",
 		})
 			.then(() => {
 				toast.success("Patch saved");
+				utils.patch.byEntityId.invalidate({ id, type });
 			})
 			.catch(() => {
 				toast.error("Failed to save patch");
 			});
 	};
 
-	const hasChanges = fileContent !== originalContent;
+	const handleMarkForDeletion = () => {
+		if (!selectedFile) return;
+		markForDeletion({ id, type, filePath: selectedFile })
+			.then(() => {
+				toast.success("File marked for deletion");
+				utils.patch.byEntityId.invalidate({ id, type });
+			})
+			.catch(() => {
+				toast.error("Failed to mark file for deletion");
+			});
+	};
+
+	const handleCreateFile = useCallback(
+		(folderPath: string, filename: string, content: string) => {
+			const filePath = folderPath ? `${folderPath}/${filename}` : filename;
+			saveAsPatch({
+				id,
+				type,
+				filePath,
+				content,
+				patchType: "create",
+			})
+				.then(() => {
+					toast.success("File created");
+					utils.patch.byEntityId.invalidate({ id, type });
+				})
+				.catch(() => {
+					toast.error("Failed to create file");
+				});
+		},
+		[id, type, saveAsPatch, utils],
+	);
+
+	const selectedFilePatch = patches?.find(
+		(p) => p.filePath === selectedFile && p.type === "delete",
+	);
+
+	const handleUnmarkDeletion = () => {
+		if (!selectedFilePatch) return;
+		updatePatch
+			.mutateAsync({
+				patchId: selectedFilePatch.patchId,
+				type: "update",
+				content: fileData || "",
+			})
+			.then(() => {
+				toast.success("Deletion unmarked");
+				utils.patch.byEntityId.invalidate({ id, type });
+			})
+			.catch(() => {
+				toast.error("Failed to unmark deletion");
+			});
+	};
+
+	const hasChanges = fileData !== undefined && fileContent !== fileData;
 
 	const renderTree = useCallback(
 		(entries: DirectoryEntry[], depth = 0) => {
@@ -114,22 +189,33 @@ export const PatchEditor = ({ id, type, repoPath, onClose }: Props) => {
 					if (entry.type === "directory") {
 						return (
 							<div key={entry.path}>
-								<button
-									type="button"
-									onClick={() => toggleFolder(entry.path)}
-									className={
-										"w-full flex items-center gap-2 px-2 py-1.5 text-sm hover:bg-muted/50 rounded-md transition-colors"
-									}
-									style={{ paddingLeft: `${depth * 12 + 8}px` }}
-								>
-									<ChevronRight
-										className={`h-4 w-4 transition-transform ${
-											isExpanded ? "rotate-90" : ""
-										}`}
+								<div className="group flex items-center">
+									<button
+										type="button"
+										onClick={() => toggleFolder(entry.path)}
+										className={
+											"flex-1 flex items-center gap-2 px-2 py-1.5 text-sm hover:bg-muted/50 rounded-md transition-colors text-left min-w-0"
+										}
+										style={{ paddingLeft: `${depth * 12 + 8}px` }}
+									>
+										<ChevronRight
+											className={`h-4 w-4 shrink-0 transition-transform ${
+												isExpanded ? "rotate-90" : ""
+											}`}
+										/>
+										<Folder className="h-4 w-4 shrink-0 text-blue-500" />
+										<span className="truncate">{entry.name}</span>
+									</button>
+									<CreateFileDialog
+										folderPath={entry.path}
+										onCreate={(filename, content) =>
+											handleCreateFile(entry.path, filename, content)
+										}
+										onOpenChange={(open) =>
+											setCreateFolderPath(open ? entry.path : null)
+										}
 									/>
-									<Folder className="h-4 w-4 text-blue-500" />
-									<span className="truncate">{entry.name}</span>
-								</button>
+								</div>
 								{isExpanded && entry.children && (
 									<div>{renderTree(entry.children, depth + 1)}</div>
 								)}
@@ -137,6 +223,10 @@ export const PatchEditor = ({ id, type, repoPath, onClose }: Props) => {
 						);
 					}
 
+					const isMarkedForDeletion = patches?.some(
+						(p) => p.filePath === entry.path && p.type === "delete",
+					);
+
 					return (
 						<button
 							type="button"
@@ -144,16 +234,19 @@ export const PatchEditor = ({ id, type, repoPath, onClose }: Props) => {
 							onClick={() => handleFileSelect(entry.path)}
 							className={`w-full flex items-center gap-2 px-2 py-1.5 text-sm hover:bg-muted/50 rounded-md transition-colors ${
 								isSelected ? "bg-muted" : ""
-							}`}
+							} ${isMarkedForDeletion ? "text-destructive" : ""}`}
 							style={{ paddingLeft: `${depth * 12 + 28}px` }}
 						>
-							<File className="h-4 w-4 text-muted-foreground" />
+							<File className="h-4 w-4 shrink-0 text-muted-foreground" />
 							<span className="truncate">{entry.name}</span>
+							{isMarkedForDeletion && (
+								<Trash2 className="h-3 w-3 shrink-0 text-destructive ml-auto" />
+							)}
 						</button>
 					);
 				});
 		},
-		[expandedFolders, selectedFile],
+		[expandedFolders, selectedFile, patches, handleCreateFile],
 	);
 
 	return (
@@ -173,18 +266,68 @@ export const PatchEditor = ({ id, type, repoPath, onClose }: Props) => {
 					</div>
 				</div>
 				{selectedFile && (
-					<Button onClick={handleSave} disabled={isSavingPatch || !hasChanges}>
-						{isSavingPatch && <Loader2 className="mr-2 h-4 w-4 animate-spin" />}
-						<Save className="mr-2 h-4 w-4" />
-						Save Patch
-					</Button>
+					<div className="flex items-center gap-2">
+						{selectedFilePatch ? (
+							<Button
+								variant="outline"
+								size="sm"
+								onClick={handleUnmarkDeletion}
+								disabled={updatePatch.isPending}
+							>
+								{updatePatch.isPending && (
+									<Loader2 className="mr-2 h-4 w-4 animate-spin" />
+								)}
+								Unmark deletion
+							</Button>
+						) : (
+							<>
+								<Button
+									variant="outline"
+									size="sm"
+									onClick={handleMarkForDeletion}
+									disabled={isMarkingDeletion}
+								>
+									{isMarkingDeletion && (
+										<Loader2 className="mr-2 h-4 w-4 animate-spin" />
+									)}
+									<Trash2 className="mr-2 h-4 w-4" />
+									Mark for deletion
+								</Button>
+								<Button
+									onClick={handleSave}
+									disabled={isSavingPatch || !hasChanges}
+								>
+									{isSavingPatch && (
+										<Loader2 className="mr-2 h-4 w-4 animate-spin" />
+									)}
+									<Save className="mr-2 h-4 w-4" />
+									Save Patch
+								</Button>
+							</>
+						)}
+					</div>
 				)}
 			</CardHeader>
 			<CardContent className="p-0">
 				<div className="grid grid-cols-[250px_1fr] border-t h-[600px]">
 					<div className="border-r h-full overflow-hidden">
 						<ScrollArea className="h-full">
-							<div className="p-2">
+							<div className="p-2 space-y-1">
+								<div className="group flex items-center gap-2 px-2 py-1.5 mb-1">
+									<CreateFileDialog
+										folderPath=""
+										alwaysVisible
+										onCreate={(filename, content) =>
+											handleCreateFile("", filename, content)
+										}
+										onOpenChange={(open) =>
+											setCreateFolderPath(open ? "" : null)
+										}
+									/>
+									<span className="text-xs text-muted-foreground">
+										New file in root
+									</span>
+								</div>
 								{isDirLoading ? (
 									<div className="flex items-center justify-center py-8">
 										<Loader2 className="h-6 w-6 animate-spin" />
diff --git a/apps/dokploy/components/dashboard/application/patches/show-patches.tsx b/apps/dokploy/components/dashboard/application/patches/show-patches.tsx
index eace7d820..1f417ecdf 100644
--- a/apps/dokploy/components/dashboard/application/patches/show-patches.tsx
+++ b/apps/dokploy/components/dashboard/application/patches/show-patches.tsx
@@ -9,6 +9,7 @@ import {
 	CardHeader,
 	CardTitle,
 } from "@/components/ui/card";
+import { Badge } from "@/components/ui/badge";
 import { Switch } from "@/components/ui/switch";
 import {
 	Table,
@@ -129,6 +130,7 @@ export const ShowPatches = ({ id, type }: Props) => {
 						<TableHeader>
 							<TableRow>
 								<TableHead>File Path</TableHead>
+								<TableHead className="w-[80px]">Type</TableHead>
 								<TableHead className="w-[100px]">Enabled</TableHead>
 								<TableHead className="w-[100px]">Actions</TableHead>
 							</TableRow>
@@ -138,10 +140,24 @@ export const ShowPatches = ({ id, type }: Props) => {
 								<TableRow key={patch.patchId}>
 									<TableCell className="font-mono text-sm">
 										<div className="flex items-center gap-2">
-											<File className="h-4 w-4 text-muted-foreground" />
+											<File className="h-4 w-4 text-muted-foreground shrink-0" />
 											{patch.filePath}
 										</div>
 									</TableCell>
+									<TableCell>
+										<Badge
+											variant={
+												patch.type === "delete"
+													? "destructive"
+													: patch.type === "create"
+														? "default"
+														: "secondary"
+											}
+											className="font-normal"
+										>
+											{patch.type}
+										</Badge>
+									</TableCell>
 									<TableCell>
 										<Switch
 											checked={patch.enabled}
@@ -169,11 +185,14 @@ export const ShowPatches = ({ id, type }: Props) => {
 									</TableCell>
 									<TableCell>
 										<div className="flex items-center gap-1">
-											<EditPatchDialog
-												patchId={patch.patchId}
-												entityId={id}
-												type={type}
-											/>
+											{(patch.type === "update" ||
+												patch.type === "create") && (
+												<EditPatchDialog
+													patchId={patch.patchId}
+													entityId={id}
+													type={type}
+												/>
+											)}
 											<Button
 												variant="ghost"
 												size="icon"
diff --git a/apps/dokploy/server/api/routers/patch.ts b/apps/dokploy/server/api/routers/patch.ts
index 9ad51c214..c53cdc7bf 100644
--- a/apps/dokploy/server/api/routers/patch.ts
+++ b/apps/dokploy/server/api/routers/patch.ts
@@ -9,6 +9,7 @@ import {
 	findPatchByFilePath,
 	findPatchById,
 	findPatchesByEntityId,
+	markPatchForDeletion,
 	readPatchRepoDirectory,
 	readPatchRepoFile,
 	updatePatch,
@@ -228,7 +229,19 @@ export const patchRouter = createTRPCRouter({
 				input.type,
 			);
 
-			if (existingPatch) {
+			// For delete patches, show current file content from repo (what will be deleted)
+			if (existingPatch?.type === "delete") {
+				try {
+					return await readPatchRepoFile(
+						input.id,
+						input.type,
+						input.filePath,
+					);
+				} catch {
+					return "(File not found in repo - will be removed if it exists)";
+				}
+			}
+			if (existingPatch?.content) {
 				return existingPatch.content;
 			}
 			return await readPatchRepoFile(input.id, input.type, input.filePath);
@@ -241,6 +254,7 @@ export const patchRouter = createTRPCRouter({
 				type: z.enum(["application", "compose"]),
 				filePath: z.string(),
 				content: z.string(),
+				patchType: z.enum(["create", "update"]).default("update"),
 			}),
 		)
 		.mutation(async ({ input, ctx }) => {
@@ -280,17 +294,59 @@ export const patchRouter = createTRPCRouter({
 			);
 
 			if (!existingPatch) {
-				const newPatch = await createPatch({
+				return await createPatch({
 					filePath: input.filePath,
 					content: input.content,
+					type: input.patchType,
 					applicationId: input.type === "application" ? input.id : undefined,
 					composeId: input.type === "compose" ? input.id : undefined,
 				});
-			} else {
-				return await updatePatch(existingPatch.patchId, {
-					content: input.content,
-				});
 			}
+
+			return await updatePatch(existingPatch.patchId, {
+				content: input.content,
+				type: input.patchType,
+			});
+		}),
+
+	markFileForDeletion: protectedProcedure
+		.input(
+			z.object({
+				id: z.string(),
+				type: z.enum(["application", "compose"]),
+				filePath: z.string(),
+			}),
+		)
+		.mutation(async ({ input, ctx }) => {
+			if (input.type === "application") {
+				const app = await findApplicationById(input.id);
+				if (
+					app.environment.project.organizationId !==
+					ctx.session.activeOrganizationId
+				) {
+					throw new TRPCError({
+						code: "UNAUTHORIZED",
+						message: "You are not authorized to access this application",
+					});
+				}
+			} else if (input.type === "compose") {
+				const compose = await findComposeById(input.id);
+				if (
+					compose.environment.project.organizationId !==
+					ctx.session.activeOrganizationId
+				) {
+					throw new TRPCError({
+						code: "UNAUTHORIZED",
+						message: "You are not authorized to access this compose",
+					});
+				}
+			}
+
+			return await markPatchForDeletion(
+				input.filePath,
+				input.id,
+				input.type,
+			);
 		}),
 
 	// Cleanup
diff --git a/packages/server/src/db/schema/patch.ts b/packages/server/src/db/schema/patch.ts
index 5e8dc1056..c4fc1abd2 100644
--- a/packages/server/src/db/schema/patch.ts
+++ b/packages/server/src/db/schema/patch.ts
@@ -56,6 +56,7 @@ export const patchRelations = relations(patch, ({ one }) => ({
 const createSchema = createInsertSchema(patch, {
 	filePath: z.string().min(1),
 	content: z.string(),
+	type: z.enum(["create", "update", "delete"]).optional(),
 	enabled: z.boolean().optional(),
 	applicationId: z.string().optional(),
 	composeId: z.string().optional(),
@@ -64,6 +65,7 @@ const createSchema = createInsertSchema(patch, {
 export const apiCreatePatch = createSchema.pick({
 	filePath: true,
 	content: true,
+	type: true,
 	enabled: true,
 	applicationId: true,
 	composeId: true,
diff --git a/packages/server/src/services/patch.ts b/packages/server/src/services/patch.ts
index fd6b29a2d..1158655e1 100644
--- a/packages/server/src/services/patch.ts
+++ b/packages/server/src/services/patch.ts
@@ -106,6 +106,26 @@ export const deletePatch = async (patchId: string) => {
 	return result[0];
 };
 
+export const markPatchForDeletion = async (
+	filePath: string,
+	entityId: string,
+	entityType: "application" | "compose",
+) => {
+	const existing = await findPatchByFilePath(filePath, entityId, entityType);
+
+	if (existing) {
+		return await updatePatch(existing.patchId, { type: "delete", content: "" });
+	}
+
+	return await createPatch({
+		filePath,
+		content: "",
+		type: "delete",
+		applicationId: entityType === "application" ? entityId : undefined,
+		composeId: entityType === "compose" ? entityId : undefined,
+	});
+};
+
 interface ApplyPatchesOptions {
 	id: string;
 	type: "application" | "compose";
@@ -133,12 +153,20 @@ export const generateApplyPatchesCommand = async ({
 
 	for (const p of patches) {
 		const filePath = join(codePath, p.filePath);
-		command += `
+
+		if (p.type === "delete") {
+			command += `
+			rm -f "${filePath}";
+			`;
+		} else {
+			// create and update: write file
+			command += `
 file="${filePath}"
 dir="$(dirname "$file")"
 mkdir -p "$dir"
 echo "${encodeBase64(p.content)}" | base64 -d > "$file"
 `;
+		}
 	}
 
 	return command;