diff --git a/plugins/config-audit/scanners/lib/active-config-reader.mjs b/plugins/config-audit/scanners/lib/active-config-reader.mjs
index d76f6af..181d47d 100644
--- a/plugins/config-audit/scanners/lib/active-config-reader.mjs
+++ b/plugins/config-audit/scanners/lib/active-config-reader.mjs
@@ -22,12 +22,27 @@ const SCHEMA_VERSION = '1.0.0';
  * Estimate tokens for a given byte count and content kind.
  * Deterministic heuristic — see feature plan §4 for rationale.
  *
+ * MCP (v5 F2): an active MCP server consumes a base overhead of ~500 tokens
+ * for protocol metadata + tool schemas, even before any tool is described.
+ * When tool count is known (Step 14 wires this up), we estimate ~200 tokens
+ * per tool description.
+ *
  * @param {number} bytes - Byte count (or item count for kind='item')
- * @param {'markdown'|'frontmatter'|'json'|'item'} kind
+ * @param {'markdown'|'frontmatter'|'json'|'item'|'mcp'} kind
+ * @param {{toolCount?: number}} [opts] - kind-specific options (mcp: toolCount)
  * @returns {number} Integer token count (rounded up)
  */
-export function estimateTokens(bytes, kind = 'markdown') {
+export function estimateTokens(bytes, kind = 'markdown', opts = {}) {
   if (kind === 'item') return 15;
+  if (kind === 'mcp') {
+    const base = 500;
+    const perTool = 200;
+    const toolCount = typeof opts.toolCount === 'number' && opts.toolCount > 0 ? opts.toolCount : 0;
+    const safeBytes = typeof bytes === 'number' && bytes > 0 && Number.isFinite(bytes) ? bytes : 0;
+    const fromBytes = Math.ceil(safeBytes / 3.5);
+    const fromTools = base + toolCount * perTool;
+    return Math.max(base, fromBytes, fromTools);
+  }
   if (typeof bytes !== 'number' || bytes < 0 || !Number.isFinite(bytes)) return 0;
   if (kind === 'frontmatter') {
     const capped = Math.min(bytes, 600);
diff --git a/plugins/config-audit/tests/lib/active-config-reader.test.mjs b/plugins/config-audit/tests/lib/active-config-reader.test.mjs
index 615ff25..e181fef 100644
--- a/plugins/config-audit/tests/lib/active-config-reader.test.mjs
+++ b/plugins/config-audit/tests/lib/active-config-reader.test.mjs
@@ -165,6 +165,31 @@ describe('estimateTokens', () => {
     assert.equal(estimateTokens(-1, 'markdown'), 0);
     assert.equal(estimateTokens(NaN, 'markdown'), 0);
   });
+
+  // v5 F2: differentiated MCP estimate
+  it('mcp: 0 bytes → at least 500 (base overhead floor)', () => {
+    assert.ok(estimateTokens(0, 'mcp') >= 500,
+      `expected >= 500, got ${estimateTokens(0, 'mcp')}`);
+  });
+
+  it('mcp: with toolCount: 10 → at least 2000', () => {
+    assert.ok(estimateTokens(0, 'mcp', { toolCount: 10 }) >= 2000,
+      `expected >= 2000, got ${estimateTokens(0, 'mcp', { toolCount: 10 })}`);
+  });
+
+  it('mcp: ratio mcp/item ≥ 30 for 10-tool server', () => {
+    const mcp = estimateTokens(0, 'mcp', { toolCount: 10 });
+    const item = estimateTokens(0, 'item');
+    assert.ok(mcp / item >= 30,
+      `expected ratio >= 30, got mcp=${mcp} item=${item} ratio=${mcp / item}`);
+  });
+
+  it('mcp: with bytes uses json-rate floor', () => {
+    // 700 bytes JSON ≈ 200 tokens, but mcp keeps 500 floor
+    assert.equal(estimateTokens(700, 'mcp'), 500);
+    // 3500 bytes JSON = 1000 tokens, exceeds floor
+    assert.equal(estimateTokens(3500, 'mcp'), 1000);
+  });
 });
 
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