diff --git a/.changeset/d1-crlf-remote-query.md b/.changeset/d1-crlf-remote-query.md
new file mode 100644
index 00000000000..6e641c4946a
--- /dev/null
+++ b/.changeset/d1-crlf-remote-query.md
@@ -0,0 +1,7 @@
+---
+"wrangler": patch
+---
+
+Normalize CRLF line endings before sending D1 commands to the remote query API
+
+`wrangler d1 migrations apply --remote` and `wrangler d1 execute --remote --command` failed with `incomplete input: SQLITE_ERROR` when the SQL contained CRLF line endings inside a compound statement such as a `CREATE TRIGGER ... BEGIN ... END;` body. The command string is now normalized to LF before it is sent to the D1 query API.
diff --git a/packages/wrangler/src/__tests__/d1/execute.test.ts b/packages/wrangler/src/__tests__/d1/execute.test.ts
index 2ced79fc5e7..d4041276d90 100644
--- a/packages/wrangler/src/__tests__/d1/execute.test.ts
+++ b/packages/wrangler/src/__tests__/d1/execute.test.ts
@@ -302,6 +302,59 @@ To continue without logging in, rerun this command with \`--temporary\`. Wrangle
 			expect(std.out).toMatch("🚣 Executed 1 command in 123.46ms");
 		});
 
+		it("should normalize CRLF line endings in commands sent to the remote query API", async ({
+			expect,
+		}) => {
+			setIsTTY(false);
+			writeWranglerConfig({
+				d1_databases: [
+					{ binding: "DATABASE", database_name: "db", database_id: "xxxx" },
+				],
+			});
+
+			msw.use(
+				...getMswSuccessMembershipHandlers([
+					{
+						id: "some-account-id",
+						name: "test-account",
+					},
+				])
+			);
+
+			let sentSql: string | undefined;
+			msw.use(
+				http.get("*/accounts/:accountId/d1/database", async () => {
+					return HttpResponse.json(
+						createFetchResult([
+							{ uuid: "xxxx", name: "db", created_at: "", version: "alpha" },
+						])
+					);
+				}),
+				http.post(
+					"*/accounts/:accountId/d1/database/:databaseId/query",
+					async ({ request }) => {
+						sentSql = ((await request.json()) as { sql: string }).sql;
+						return HttpResponse.json(
+							createFetchResult([
+								{
+									results: [{ result: 1 }],
+									success: true,
+									meta: { duration: 100 },
+								},
+							])
+						);
+					}
+				)
+			);
+
+			await runWrangler(
+				"d1 execute db --remote --command 'CREATE TRIGGER trg BEFORE DELETE ON probe_z\r\nBEGIN\r\n  SELECT RAISE(ABORT, '\''no'\'');\r\nEND;'"
+			);
+
+			expect(sentSql).toBeDefined();
+			expect(sentSql).not.toContain("\r");
+		});
+
 		it("should format batch execution duration with 2 decimal places", async ({
 			expect,
 		}) => {
diff --git a/packages/wrangler/src/d1/execute.ts b/packages/wrangler/src/d1/execute.ts
index 290a0a64fbb..f1dc9d450a6 100644
--- a/packages/wrangler/src/d1/execute.ts
+++ b/packages/wrangler/src/d1/execute.ts
@@ -503,14 +503,17 @@ async function executeRemotely({
 			},
 		];
 	} else {
+		// The D1 query API splits multi-statement SQL on `;` server-side, and
+		// mishandles CRLF line endings inside compound statements such as a
+		// `CREATE TRIGGER ... BEGIN ... END;` body (issue #14991). Normalize
+		// to LF so the server receives the same input that works for LF files.
+		const sql = input.command?.replace(/\r\n/g, "\n");
 		const result = await d1ApiPost<QueryResult[]>(
 			config,
 			accountId,
 			db,
 			"query",
-			{
-				sql: input.command,
-			}
+			{ sql }
 		);
 		logResult(result);
 		return result;