diff --git a/drizzle-kit/src/sqlgenerator.ts b/drizzle-kit/src/sqlgenerator.ts
index 64d3c4063c..680cab58f1 100644
--- a/drizzle-kit/src/sqlgenerator.ts
+++ b/drizzle-kit/src/sqlgenerator.ts
@@ -2407,7 +2407,7 @@ export class LibSQLModifyColumn extends Convertor {
 		for (const table of Object.values(json2.tables)) {
 			for (const index of Object.values(table.indexes)) {
 				const unsquashed = SQLiteSquasher.unsquashIdx(index);
-				sqlStatements.push(`DROP INDEX "${unsquashed.name}";`);
+				sqlStatements.push(`DROP INDEX IF EXISTS "${unsquashed.name}";`);
 				indexes.push({ ...unsquashed, tableName: table.name });
 			}
 		}
@@ -2473,7 +2473,7 @@ export class LibSQLModifyColumn extends Convertor {
 			const tableName = index.tableName;
 
 			sqlStatements.push(
-				`CREATE ${indexPart} \`${index.name}\` ON \`${tableName}\` (${uniqueString})${whereStatement};`,
+				`CREATE ${indexPart} IF NOT EXISTS \`${index.name}\` ON \`${tableName}\` (${uniqueString})${whereStatement};`,
 			);
 		}
 
@@ -3735,7 +3735,7 @@ export class SqliteDropIndexConvertor extends Convertor {
 
 	convert(statement: JsonDropIndexStatement): string {
 		const { name } = PgSquasher.unsquashIdx(statement.data);
-		return `DROP INDEX \`${name}\`;`;
+		return `DROP INDEX IF EXISTS \`${name}\`;`;
 	}
 }
 
diff --git a/drizzle-kit/tests/libsql-statements.test.ts b/drizzle-kit/tests/libsql-statements.test.ts
index 636496c458..95b496b654 100644
--- a/drizzle-kit/tests/libsql-statements.test.ts
+++ b/drizzle-kit/tests/libsql-statements.test.ts
@@ -917,13 +917,13 @@ test('set not null with index', async (t) => {
 
 	expect(sqlStatements.length).toBe(3);
 	expect(sqlStatements[0]).toBe(
-		`DROP INDEX "users_name_index";`,
+		`DROP INDEX IF EXISTS "users_name_index";`,
 	);
 	expect(sqlStatements[1]).toBe(
 		`ALTER TABLE \`users\` ALTER COLUMN "name" TO "name" text NOT NULL;`,
 	);
 	expect(sqlStatements[2]).toBe(
-		`CREATE INDEX \`users_name_index\` ON \`users\` (\`name\`);`,
+		`CREATE INDEX IF NOT EXISTS \`users_name_index\` ON \`users\` (\`name\`);`,
 	);
 });
 
@@ -972,18 +972,18 @@ test('drop not null with two indexes', async (t) => {
 
 	expect(sqlStatements.length).toBe(5);
 	expect(sqlStatements[0]).toBe(
-		`DROP INDEX "users_name_unique";`,
+		`DROP INDEX IF EXISTS "users_name_unique";`,
 	);
 	expect(sqlStatements[1]).toBe(
-		`DROP INDEX "users_age_index";`,
+		`DROP INDEX IF EXISTS "users_age_index";`,
 	);
 	expect(sqlStatements[2]).toBe(
 		`ALTER TABLE \`users\` ALTER COLUMN "name" TO "name" text;`,
 	);
 	expect(sqlStatements[3]).toBe(
-		`CREATE UNIQUE INDEX \`users_name_unique\` ON \`users\` (\`name\`);`,
+		`CREATE UNIQUE INDEX IF NOT EXISTS \`users_name_unique\` ON \`users\` (\`name\`);`,
 	);
 	expect(sqlStatements[4]).toBe(
-		`CREATE INDEX \`users_age_index\` ON \`users\` (\`age\`);`,
+		`CREATE INDEX IF NOT EXISTS \`users_age_index\` ON \`users\` (\`age\`);`,
 	);
 });
diff --git a/drizzle-kit/tests/push/libsql.test.ts b/drizzle-kit/tests/push/libsql.test.ts
index 2ae2e38110..bf7e59bd90 100644
--- a/drizzle-kit/tests/push/libsql.test.ts
+++ b/drizzle-kit/tests/push/libsql.test.ts
@@ -185,7 +185,7 @@ test('added, dropped index', async (t) => {
 
 	expect(sqlStatements.length).toBe(2);
 	expect(sqlStatements[0]).toBe(
-		`DROP INDEX \`customers_address_unique\`;`,
+		`DROP INDEX IF EXISTS \`customers_address_unique\`;`,
 	);
 	expect(sqlStatements[1]).toBe(
 		`CREATE UNIQUE INDEX \`customers_is_confirmed_unique\` ON \`customers\` (\`is_confirmed\`);`,
@@ -963,13 +963,13 @@ test('set not null with index', async (t) => {
 
 	expect(sqlStatements.length).toBe(3);
 	expect(sqlStatements[0]).toBe(
-		`DROP INDEX "users_name_index";`,
+		`DROP INDEX IF EXISTS "users_name_index";`,
 	);
 	expect(sqlStatements[1]).toBe(
 		`ALTER TABLE \`users\` ALTER COLUMN "name" TO "name" text NOT NULL;`,
 	);
 	expect(sqlStatements[2]).toBe(
-		`CREATE INDEX \`users_name_index\` ON \`users\` (\`name\`);`,
+		`CREATE INDEX IF NOT EXISTS \`users_name_index\` ON \`users\` (\`name\`);`,
 	);
 	expect(columnsToRemove!.length).toBe(0), expect(infoToPrint!.length).toBe(0);
 	expect(shouldAskForApprove).toBe(false);
@@ -1035,19 +1035,19 @@ test('drop not null with two indexes', async (t) => {
 
 	expect(sqlStatements.length).toBe(5);
 	expect(sqlStatements[0]).toBe(
-		`DROP INDEX "users_name_unique";`,
+		`DROP INDEX IF EXISTS "users_name_unique";`,
 	);
 	expect(sqlStatements[1]).toBe(
-		`DROP INDEX "users_age_index";`,
+		`DROP INDEX IF EXISTS "users_age_index";`,
 	);
 	expect(sqlStatements[2]).toBe(
 		`ALTER TABLE \`users\` ALTER COLUMN "name" TO "name" text;`,
 	);
 	expect(sqlStatements[3]).toBe(
-		`CREATE UNIQUE INDEX \`users_name_unique\` ON \`users\` (\`name\`);`,
+		`CREATE UNIQUE INDEX IF NOT EXISTS \`users_name_unique\` ON \`users\` (\`name\`);`,
 	);
 	expect(sqlStatements[4]).toBe(
-		`CREATE INDEX \`users_age_index\` ON \`users\` (\`age\`);`,
+		`CREATE INDEX IF NOT EXISTS \`users_age_index\` ON \`users\` (\`age\`);`,
 	);
 	expect(columnsToRemove!.length).toBe(0), expect(infoToPrint!.length).toBe(0);
 	expect(shouldAskForApprove).toBe(false);
@@ -1055,6 +1055,73 @@ test('drop not null with two indexes', async (t) => {
 	expect(tablesToTruncate!.length).toBe(0);
 });
 
+test('set not null on two tables with indexes in one push (#5564)', async (t) => {
+	const turso = createClient({
+		url: ':memory:',
+	});
+
+	const schema1 = {
+		users: sqliteTable('users', {
+			id: text('id').primaryKey(),
+			email: text('email').notNull(),
+			name: text('name'),
+		}, (table) => ({
+			emailIdx: uniqueIndex('users_email_idx').on(table.email),
+		})),
+		projects: sqliteTable('projects', {
+			id: text('id').primaryKey(),
+			ownerId: text('owner_id').notNull(),
+			title: text('title'),
+		}, (table) => ({
+			ownerIdx: index('projects_owner_idx').on(table.ownerId),
+		})),
+	};
+
+	const schema2 = {
+		users: sqliteTable('users', {
+			id: text('id').primaryKey(),
+			email: text('email').notNull(),
+			name: text('name').notNull(),
+		}, (table) => ({
+			emailIdx: uniqueIndex('users_email_idx').on(table.email),
+		})),
+		projects: sqliteTable('projects', {
+			id: text('id').primaryKey(),
+			ownerId: text('owner_id').notNull(),
+			title: text('title').notNull(),
+		}, (table) => ({
+			ownerIdx: index('projects_owner_idx').on(table.ownerId),
+		})),
+	};
+
+	const {
+		statements,
+		sqlStatements,
+		columnsToRemove,
+		infoToPrint,
+		shouldAskForApprove,
+		tablesToRemove,
+		tablesToTruncate,
+	} = await diffTestSchemasPushLibSQL(
+		turso,
+		schema1,
+		schema2,
+		[],
+	);
+
+	expect(statements!.length).toBe(2);
+	expect(statements!.every((s) => s.type === 'alter_table_alter_column_set_notnull')).toBe(true);
+
+	const dropLines = sqlStatements.filter((s) => s.startsWith('DROP INDEX'));
+	expect(dropLines.every((s) => s.includes('IF EXISTS'))).toBe(true);
+
+	expect(columnsToRemove!.length).toBe(0);
+	expect(infoToPrint!.length).toBe(0);
+	expect(shouldAskForApprove).toBe(false);
+	expect(tablesToRemove!.length).toBe(0);
+	expect(tablesToTruncate!.length).toBe(0);
+});
+
 test('add check constraint to table', async (t) => {
 	const turso = createClient({
 		url: ':memory:',
diff --git a/drizzle-kit/tests/push/sqlite.test.ts b/drizzle-kit/tests/push/sqlite.test.ts
index e2c85233a3..dd1d88fe3a 100644
--- a/drizzle-kit/tests/push/sqlite.test.ts
+++ b/drizzle-kit/tests/push/sqlite.test.ts
@@ -185,7 +185,7 @@ test('dropped, added unique index', async (t) => {
 
 	expect(sqlStatements.length).toBe(2);
 	expect(sqlStatements[0]).toBe(
-		`DROP INDEX \`customers_address_unique\`;`,
+		`DROP INDEX IF EXISTS \`customers_address_unique\`;`,
 	);
 	expect(sqlStatements[1]).toBe(
 		`CREATE UNIQUE INDEX \`customers_is_confirmed_unique\` ON \`customers\` (\`is_confirmed\`);`,