diff --git a/.changeset/nine-bugs-camp.md b/.changeset/nine-bugs-camp.md
new file mode 100644
index 000000000..1a817964e
--- /dev/null
+++ b/.changeset/nine-bugs-camp.md
@@ -0,0 +1,5 @@
+---
+"bits-ui": patch
+---
+
+fix(Command): item selection logic
diff --git a/packages/bits-ui/src/lib/bits/command/command.svelte.ts b/packages/bits-ui/src/lib/bits/command/command.svelte.ts
index 9c0c631ca..8be7c6157 100644
--- a/packages/bits-ui/src/lib/bits/command/command.svelte.ts
+++ b/packages/bits-ui/src/lib/bits/command/command.svelte.ts
@@ -148,7 +148,7 @@ export class CommandRootState {
 		if (key === "search") {
 			// Filter synchronously before emitting back to children
 			this.#filterItems();
-			this.#sort();
+			this.#sort({ forceSelectFirst: value === "" && !this.#isInitialMount });
 		} else if (key === "value") {
 			if (!preventScroll) this.#scrollSelectedIntoView();
 		}
@@ -185,13 +185,13 @@ export class CommandRootState {
 	/**
 	 * Sorts items and groups based on search scores.
 	 * Groups are sorted by their highest scoring item.
-	 * When no search active, selects first item.
+	 * When no search is active, preserves the current item unless a reset is requested.
 	 */
-	#sort(): void {
+	#sort(opts: { forceSelectFirst?: boolean } = {}): void {
 		if (!this._commandState.search || this.opts.shouldFilter.current === false) {
 			// if no search and no initial value set or when clearing search,
 			// we select the first item.
-			if (!this._commandState.value || !this.#isInitialMount) {
+			if (!this._commandState.value || opts.forceSelectFirst) {
 				this.#selectFirstItem();
 			} else if (this.#isInitialMount && this._commandState.value) {
 				// scroll the initial value into view if it exists
@@ -300,6 +300,20 @@ export class CommandRootState {
 		});
 	}
 
+	#selectFirstItemIfValueMissing(value: string): void {
+		afterTick(() => {
+			if (this._commandState.value !== value) return;
+
+			const selectedItemExists = this.getValidItems().some(
+				(item) => item.getAttribute(COMMAND_VALUE_ATTR) === value
+			);
+
+			if (!selectedItemExists) {
+				this.#selectFirstItem();
+			}
+		});
+	}
+
 	/**
 	 * Scrolls the initial value into view if it exists and is not the first item.
 	 * Called during initial mount when a value is provided.
@@ -675,10 +689,13 @@ export class CommandRootState {
 
 			this.#filterItems();
 
-			// The item removed have been the selected one,
-			// so selection should be moved to the first
 			if (selectedItem?.getAttribute("id") === id) {
-				this.#selectFirstItem();
+				const selectedValue = selectedItem.getAttribute(COMMAND_VALUE_ATTR);
+				if (selectedValue) {
+					this.#selectFirstItemIfValueMissing(selectedValue);
+				} else {
+					this.#selectFirstItem();
+				}
 			}
 
 			this.#scheduleUpdate();
diff --git a/tests/src/tests/command/command-rerender-test.svelte b/tests/src/tests/command/command-rerender-test.svelte
new file mode 100644
index 000000000..b52431422
--- /dev/null
+++ b/tests/src/tests/command/command-rerender-test.svelte
@@ -0,0 +1,39 @@
+<script lang="ts">
+	import { Command } from "bits-ui";
+	import type { ComponentProps } from "svelte";
+
+	let { ...rest }: ComponentProps<typeof Command.Root> = $props();
+
+	const statuses = ["Backlog", "Todo", "Done", "Canceled"];
+	let selectedStatuses = $state<string[]>([]);
+	let itemRenderKey = $state(0);
+
+	function toggleStatus(status: string) {
+		selectedStatuses = selectedStatuses.includes(status)
+			? selectedStatuses.filter((value) => value !== status)
+			: [...selectedStatuses, status];
+		itemRenderKey++;
+	}
+</script>
+
+<Command.Root {...rest} data-testid="root">
+	<Command.Input data-testid="input" aria-label="Search" />
+	<Command.List data-testid="list">
+		<Command.Viewport data-testid="viewport">
+			{#key itemRenderKey}
+				{#each statuses as status (status)}
+					<Command.Item
+						value={status}
+						data-testid={`item-${status.toLowerCase()}`}
+						onSelect={() => toggleStatus(status)}
+					>
+						<span data-testid={`selected-${status.toLowerCase()}`}>
+							{selectedStatuses.includes(status) ? "selected" : ""}
+						</span>
+						{status}
+					</Command.Item>
+				{/each}
+			{/key}
+		</Command.Viewport>
+	</Command.List>
+</Command.Root>
diff --git a/tests/src/tests/command/command.browser.test.ts b/tests/src/tests/command/command.browser.test.ts
index df894036e..48eb8eb92 100644
--- a/tests/src/tests/command/command.browser.test.ts
+++ b/tests/src/tests/command/command.browser.test.ts
@@ -4,6 +4,7 @@ import { render } from "vitest-browser-svelte";
 import type { ComponentProps } from "svelte";
 import { getTestKbd } from "../utils.js";
 import CommandTest from "./command-test.svelte";
+import CommandRerenderTest from "./command-rerender-test.svelte";
 import { expectExists, expectNotExists } from "../browser-utils";
 
 const kbd = getTestKbd();
@@ -22,6 +23,16 @@ function setup(props: Partial<ComponentProps<typeof CommandTest>> = {}) {
 	};
 }
 
+function setupRerenderTest(props: Partial<ComponentProps<typeof CommandRerenderTest>> = {}) {
+	// oxlint-disable-next-line no-explicit-any
+	const returned = render(CommandRerenderTest, props as any);
+	const input = page.getByTestId("input");
+	return {
+		...returned,
+		input,
+	};
+}
+
 it("should select the first item by default", async () => {
 	setup();
 
@@ -52,6 +63,19 @@ it("should respect initial value for items in the first group", async () => {
 	await expect.element(page.getByText("Introduction")).not.toHaveAttribute("data-selected");
 });
 
+it("should keep the clicked item active on initial click", async () => {
+	const t = setupRerenderTest();
+
+	await userEvent.click(page.getByTestId("item-done"));
+	await expect.element(page.getByTestId("selected-done")).toHaveTextContent("selected");
+	await expect.element(page.getByText("Done")).toHaveAttribute("data-selected");
+	await expect.element(page.getByText("Backlog")).not.toHaveAttribute("data-selected");
+
+	(t.input.element() as HTMLElement).focus();
+	await userEvent.keyboard(kbd.ARROW_DOWN);
+	await expect.element(page.getByText("Canceled")).toHaveAttribute("data-selected");
+});
+
 it("should render the separator when search is empty and remove it when search is not empty", async () => {
 	const t = setup();