diff --git a/AgentCompany-New/src/renderer/src/pages/FilesPage.tsx b/AgentCompany-New/src/renderer/src/pages/FilesPage.tsx
index a2108797..3d599cb0 100644
--- a/AgentCompany-New/src/renderer/src/pages/FilesPage.tsx
+++ b/AgentCompany-New/src/renderer/src/pages/FilesPage.tsx
@@ -32,7 +32,7 @@ export function FilesPage({ snapshot, actions }: PageProps) {
   const [view, setView] = useState<ViewMode>("list");
   const [scanFilter, setScanFilter] = useState<FileScanState | "all">("all");
 
-  const departments = collectDepartments(agents);
+  const departments = collectDepartments(files, agents);
   const filesByAgent = collectAgentFiles(files, agents);
   const sectionFiles = filterFiles(files, section, agents);
   const visibleFiles = scanFilter === "all" ? sectionFiles : sectionFiles.filter((file) => file.scanState === scanFilter);
diff --git a/AgentCompany-New/src/renderer/src/pages/files/FilesTree.tsx b/AgentCompany-New/src/renderer/src/pages/files/FilesTree.tsx
index 529f6406..127b87af 100644
--- a/AgentCompany-New/src/renderer/src/pages/files/FilesTree.tsx
+++ b/AgentCompany-New/src/renderer/src/pages/files/FilesTree.tsx
@@ -91,7 +91,7 @@ function TreeItem({
 }) {
   return (
     <button type="button" className={`nav-item ${active ? "active" : ""}`.trim()} onClick={onClick}>
-      <Icon name={icon} size={14} />
+      <span className="icon-box"><Icon name={icon} size={18} /></span>
       <span>{label}</span>
       <span className="nav-badge num">{count}</span>
     </button>
diff --git a/AgentCompany-New/src/renderer/src/pages/files/file-helpers.ts b/AgentCompany-New/src/renderer/src/pages/files/file-helpers.ts
index 44849ba0..edac1934 100644
--- a/AgentCompany-New/src/renderer/src/pages/files/file-helpers.ts
+++ b/AgentCompany-New/src/renderer/src/pages/files/file-helpers.ts
@@ -23,13 +23,19 @@ export const FILE_COLOR_MAP: Record<string, { color: string; label: string }> =
   folder: { color: "#a1a1aa", label: "" },
 };
 
-export function collectDepartments(agents: AgentRecord[]): Array<{ name: string; count: number }> {
-  const seen = new Map<string, number>();
-  for (const agent of agents) {
-    if (!agent.department) continue;
-    seen.set(agent.department, (seen.get(agent.department) ?? 0) + 1);
+/** Departments shown in the file tree carry a FILE count, not an agent count:
+ * the badge must equal what opening the section reveals. Departments with no
+ * files are omitted so the tree never advertises a folder that opens empty. */
+export function collectDepartments(files: FileObjectRecord[], agents: AgentRecord[]): Array<{ name: string; count: number }> {
+  const departmentByAgent = new Map(agents.map((agent) => [agent.id, agent.department]));
+  const counts = new Map<string, number>();
+  for (const file of files) {
+    if (file.ownerType !== "agent" || !file.ownerId) continue;
+    const department = departmentByAgent.get(file.ownerId);
+    if (!department) continue;
+    counts.set(department, (counts.get(department) ?? 0) + 1);
   }
-  return [...seen.entries()].map(([name, count]) => ({ name, count })).sort((a, b) => a.name.localeCompare(b.name));
+  return [...counts.entries()].map(([name, count]) => ({ name, count })).sort((a, b) => a.name.localeCompare(b.name));
 }
 
 export function collectAgentFiles(files: FileObjectRecord[], agents: AgentRecord[]): Array<{ agent: AgentRecord; count: number }> {
diff --git a/AgentCompany-New/tests/unit/file-helpers.test.ts b/AgentCompany-New/tests/unit/file-helpers.test.ts
new file mode 100644
index 00000000..343ec0fc
--- /dev/null
+++ b/AgentCompany-New/tests/unit/file-helpers.test.ts
@@ -0,0 +1,41 @@
+import { describe, expect, test } from "vitest";
+import { collectDepartments } from "../../src/renderer/src/pages/files/file-helpers";
+import type { AgentRecord, FileObjectRecord } from "../../src/shared/domain";
+
+function agent(id: string, department: string): AgentRecord {
+  return {
+    id, orgId: "org", name: id, role: "engineer", department,
+    modelProviderId: null, modelId: null, budgetCents: 0, managerAgentId: null,
+    title: id, roleLevel: "ic", modelStrategy: "single", workspaceId: null,
+    heartbeatEnabled: false, heartbeatIntervalSec: 0, lifecycle: "active", createdAt: "2026-01-01",
+  };
+}
+
+function file(id: string, ownerType: FileObjectRecord["ownerType"], ownerId: string | null): FileObjectRecord {
+  return {
+    id, orgId: "org", name: id, kind: "doc", sizeBytes: 1, sha256: "x", storagePath: `/tmp/${id}`,
+    ownerType, ownerId, spaceId: null, pinned: false, scanState: "approved", scanLabelsJson: "[]",
+    scannedAt: null, createdAt: "2026-01-01", updatedAt: null,
+  };
+}
+
+describe("collectDepartments", () => {
+  test("counts files per department, not agents, and omits empty departments", () => {
+    const agents = [agent("a1", "Engineering"), agent("a2", "Engineering"), agent("a3", "Design"), agent("a4", "Sales")];
+    const files = [
+      file("f1", "agent", "a1"),
+      file("f2", "agent", "a1"),
+      file("f3", "agent", "a3"),
+      file("f4", "employee", "emp1"), // not owned by an agent → ignored
+    ];
+    // Engineering has two agents but only a1 holds files (2); Design has 1; Sales has agents but no files.
+    expect(collectDepartments(files, agents)).toEqual([
+      { name: "Design", count: 1 },
+      { name: "Engineering", count: 2 },
+    ]);
+  });
+
+  test("returns nothing when no agent owns a file", () => {
+    expect(collectDepartments([], [agent("a1", "Engineering")])).toEqual([]);
+  });
+});