diff --git a/airflow-core/src/airflow/ui/src/components/FilterBar/FilterBar.test.tsx b/airflow-core/src/airflow/ui/src/components/FilterBar/FilterBar.test.tsx
new file mode 100644
index 0000000000000..d4469e41142ab
--- /dev/null
+++ b/airflow-core/src/airflow/ui/src/components/FilterBar/FilterBar.test.tsx
@@ -0,0 +1,62 @@
+/*!
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+import "@testing-library/jest-dom/vitest";
+import { render, screen, waitFor } from "@testing-library/react";
+import { describe, expect, it, vi } from "vitest";
+
+import { ChakraWrapper } from "src/utils/ChakraWrapper.tsx";
+
+import { FilterBar } from "./FilterBar";
+import type { FilterConfig } from "./types";
+
+const configs: Array<FilterConfig> = [
+  {
+    key: "state",
+    label: "State",
+    type: "text",
+  },
+];
+
+const getPillText = (value: string) => {
+  const matches = screen.getAllByText((_, element) => element?.textContent === `State: ${value}`);
+
+  return matches[matches.length - 1];
+};
+
+const queryPillText = (value: string) =>
+  screen.queryAllByText((_, element) => element?.textContent === `State: ${value}`).at(-1);
+
+describe("FilterBar", () => {
+  it("updates existing pills when initial values change", async () => {
+    const onFiltersChange = vi.fn();
+    const { rerender } = render(
+      <FilterBar configs={configs} initialValues={{ state: "queued" }} onFiltersChange={onFiltersChange} />,
+      { wrapper: ChakraWrapper },
+    );
+
+    expect(getPillText("queued")).toBeInTheDocument();
+
+    rerender(
+      <FilterBar configs={configs} initialValues={{ state: "running" }} onFiltersChange={onFiltersChange} />,
+    );
+
+    await waitFor(() => expect(getPillText("running")).toBeInTheDocument());
+    expect(queryPillText("queued")).toBeUndefined();
+  });
+});
diff --git a/airflow-core/src/airflow/ui/src/components/FilterBar/FilterBar.tsx b/airflow-core/src/airflow/ui/src/components/FilterBar/FilterBar.tsx
index eed230bc98e86..a63f858842a3d 100644
--- a/airflow-core/src/airflow/ui/src/components/FilterBar/FilterBar.tsx
+++ b/airflow-core/src/airflow/ui/src/components/FilterBar/FilterBar.tsx
@@ -38,6 +38,14 @@ const defaultInitialValues: Record<string, FilterValue> = {};
 const getFilterIcon = (config: FilterConfig): React.ReactNode =>
   config.icon ?? getDefaultFilterIcon(config.type);
 
+const areFilterValuesEqual = (left: FilterValue, right: FilterValue) => {
+  try {
+    return JSON.stringify(left) === JSON.stringify(right);
+  } catch {
+    return Object.is(left, right);
+  }
+};
+
 export const FilterBar = ({
   configs,
   initialValues = defaultInitialValues,
@@ -84,23 +92,40 @@ export const FilterBar = ({
     }
 
     setFilters((prevFilters) => {
-      // Use a Set to avoid O(n²) lookup when checking for existing pills.
-      const existingKeys = new Set(prevFilters.map((filter) => filter.config.key));
-      const toAdd = pillsToAdd.filter((pill) => !existingKeys.has(pill.config.key));
+      const pillsByKey = new Map(pillsToAdd.map((pill) => [pill.config.key, pill]));
 
-      // Remove pills that had a committed value but whose URL param was cleared externally.
-      const afterRemove = prevFilters.filter((filter) => {
-        const pillHadValue = isValidFilterValue(filter.config.type, filter.value);
-        const urlValue = initialValues[filter.config.key];
+      const reconciledFilters = prevFilters.flatMap((filter) => {
+        const pill = pillsByKey.get(filter.config.key);
 
-        return !pillHadValue || isValidFilterValue(filter.config.type, urlValue);
+        if (pill === undefined) {
+          const pillHadValue = isValidFilterValue(filter.config.type, filter.value);
+          const urlValue = initialValues[filter.config.key];
+
+          if (pillHadValue && !isValidFilterValue(filter.config.type, urlValue)) {
+            return [];
+          }
+
+          return [filter];
+        }
+
+        if (areFilterValuesEqual(filter.value, pill.value)) {
+          return [filter];
+        }
+
+        return [{ ...filter, value: pill.value }];
       });
 
-      if (toAdd.length === 0 && afterRemove.length === prevFilters.length) {
+      const existingKeys = new Set(prevFilters.map((filter) => filter.config.key));
+      const toAdd = pillsToAdd.filter((pill) => !existingKeys.has(pill.config.key));
+      const hasReconciledChanges =
+        reconciledFilters.length !== prevFilters.length ||
+        reconciledFilters.some((filter, index) => filter !== prevFilters[index]);
+
+      if (!hasReconciledChanges && toAdd.length === 0) {
         return prevFilters;
       }
 
-      return [...afterRemove, ...toAdd];
+      return [...reconciledFilters, ...toAdd];
     });
     // configs is intentionally omitted — it is structurally stable across renders and including
     // it would risk infinite re-render loops. initialValuesKey captures all relevant URL changes.