diff --git a/src/auto-reply/reply/agent-runner.messaging-tools.test.ts b/src/auto-reply/reply/agent-runner.messaging-tools.test.ts
index ecbcd8e18..394aeb991 100644
--- a/src/auto-reply/reply/agent-runner.messaging-tools.test.ts
+++ b/src/auto-reply/reply/agent-runner.messaging-tools.test.ts
@@ -1,6 +1,10 @@
+import fs from "node:fs/promises";
+import os from "node:os";
+import path from "node:path";
 import { describe, expect, it, vi } from "vitest";
 
 import type { TemplateContext } from "../templating.js";
+import { loadSessionStore, saveSessionStore, type SessionEntry } from "../../config/sessions.js";
 import type { FollowupRun, QueueSettings } from "./queue.js";
 import { createMockTypingController } from "./test-helpers.js";
 
@@ -38,8 +42,12 @@ vi.mock("./queue.js", async () => {
 
 import { runReplyAgent } from "./agent-runner.js";
 
-function createRun(messageProvider = "slack") {
+function createRun(
+  messageProvider = "slack",
+  opts: { storePath?: string; sessionKey?: string } = {},
+) {
   const typing = createMockTypingController();
+  const sessionKey = opts.sessionKey ?? "main";
   const sessionCtx = {
     Provider: messageProvider,
     OriginatingTo: "channel:C1",
@@ -53,7 +61,7 @@ function createRun(messageProvider = "slack") {
     enqueuedAt: Date.now(),
     run: {
       sessionId: "session",
-      sessionKey: "main",
+      sessionKey,
       messageProvider,
       sessionFile: "/tmp/session.jsonl",
       workspaceDir: "/tmp",
@@ -85,6 +93,8 @@ function createRun(messageProvider = "slack") {
     isStreaming: false,
     typing,
     sessionCtx,
+    sessionKey,
+    storePath: opts.storePath,
     defaultModel: "anthropic/claude-opus-4-5",
     resolvedVerboseLevel: "off",
     isNewSession: false,
@@ -141,4 +151,34 @@ describe("runReplyAgent messaging tool suppression", () => {
 
     expect(result).toMatchObject({ text: "hello world!" });
   });
+
+  it("persists usage even when replies are suppressed", async () => {
+    const storePath = path.join(
+      await fs.mkdtemp(path.join(os.tmpdir(), "clawdbot-session-store-")),
+      "sessions.json",
+    );
+    const sessionKey = "main";
+    const entry: SessionEntry = { sessionId: "session", updatedAt: Date.now() };
+    await saveSessionStore(storePath, { [sessionKey]: entry });
+
+    runEmbeddedPiAgentMock.mockResolvedValueOnce({
+      payloads: [{ text: "hello world!" }],
+      messagingToolSentTexts: ["different message"],
+      messagingToolSentTargets: [{ tool: "slack", provider: "slack", to: "channel:C1" }],
+      meta: {
+        agentMeta: {
+          usage: { input: 10, output: 5 },
+          model: "claude-opus-4-5",
+          provider: "anthropic",
+        },
+      },
+    });
+
+    const result = await createRun("slack", { storePath, sessionKey });
+
+    expect(result).toBeUndefined();
+    const store = loadSessionStore(storePath, { skipCache: true });
+    expect(store[sessionKey]?.totalTokens ?? 0).toBeGreaterThan(0);
+    expect(store[sessionKey]?.model).toBe("claude-opus-4-5");
+  });
 });
diff --git a/src/auto-reply/reply/agent-runner.ts b/src/auto-reply/reply/agent-runner.ts
index 1aeb8e78f..dec2d789a 100644
--- a/src/auto-reply/reply/agent-runner.ts
+++ b/src/auto-reply/reply/agent-runner.ts
@@ -1,6 +1,5 @@
 import crypto from "node:crypto";
 import fs from "node:fs";
-import { setCliSessionId } from "../../agents/cli-session.js";
 import { lookupContextTokens } from "../../agents/context.js";
 import { DEFAULT_CONTEXT_TOKENS } from "../../agents/defaults.js";
 import { resolveModelAuthMode } from "../../agents/model-auth.js";
@@ -38,6 +37,7 @@ import { resolveBlockStreamingCoalescing } from "./block-streaming.js";
 import { createFollowupRunner } from "./followup-runner.js";
 import { enqueueFollowupRun, type FollowupRun, type QueueSettings } from "./queue.js";
 import { createReplyToModeFilterForChannel, resolveReplyToMode } from "./reply-threading.js";
+import { persistSessionUsageUpdate } from "./session-usage.js";
 import { incrementCompactionCount } from "./session-updates.js";
 import type { TypingController } from "./typing.js";
 import { createTypingSignaler } from "./typing-mode.js";
@@ -365,6 +365,30 @@ export async function runReplyAgent(params: {
       await Promise.allSettled(pendingToolTasks);
     }
 
+    const usage = runResult.meta.agentMeta?.usage;
+    const modelUsed = runResult.meta.agentMeta?.model ?? fallbackModel ?? defaultModel;
+    const providerUsed =
+      runResult.meta.agentMeta?.provider ?? fallbackProvider ?? followupRun.run.provider;
+    const cliSessionId = isCliProvider(providerUsed, cfg)
+      ? runResult.meta.agentMeta?.sessionId?.trim()
+      : undefined;
+    const contextTokensUsed =
+      agentCfgContextTokens ??
+      lookupContextTokens(modelUsed) ??
+      activeSessionEntry?.contextTokens ??
+      DEFAULT_CONTEXT_TOKENS;
+
+    await persistSessionUsageUpdate({
+      storePath,
+      sessionKey,
+      usage,
+      modelUsed,
+      providerUsed,
+      contextTokensUsed,
+      systemPromptReport: runResult.meta.systemPromptReport,
+      cliSessionId,
+    });
+
     // Drain any late tool/block deliveries before deciding there's "nothing to send".
     // Otherwise, a late typing trigger (e.g. from a tool callback) can outlive the run and
     // keep the typing indicator stuck.
@@ -395,19 +419,6 @@ export async function runReplyAgent(params: {
 
     await signalTypingIfNeeded(replyPayloads, typingSignals);
 
-    const usage = runResult.meta.agentMeta?.usage;
-    const modelUsed = runResult.meta.agentMeta?.model ?? fallbackModel ?? defaultModel;
-    const providerUsed =
-      runResult.meta.agentMeta?.provider ?? fallbackProvider ?? followupRun.run.provider;
-    const cliSessionId = isCliProvider(providerUsed, cfg)
-      ? runResult.meta.agentMeta?.sessionId?.trim()
-      : undefined;
-    const contextTokensUsed =
-      agentCfgContextTokens ??
-      lookupContextTokens(modelUsed) ??
-      activeSessionEntry?.contextTokens ??
-      DEFAULT_CONTEXT_TOKENS;
-
     if (isDiagnosticsEnabled(cfg) && hasNonzeroUsage(usage)) {
       const input = usage.input ?? 0;
       const output = usage.output ?? 0;
@@ -445,72 +456,6 @@ export async function runReplyAgent(params: {
       });
     }
 
-    if (storePath && sessionKey) {
-      if (hasNonzeroUsage(usage)) {
-        try {
-          await updateSessionStoreEntry({
-            storePath,
-            sessionKey,
-            update: async (entry) => {
-              const input = usage.input ?? 0;
-              const output = usage.output ?? 0;
-              const promptTokens = input + (usage.cacheRead ?? 0) + (usage.cacheWrite ?? 0);
-              const patch: Partial<SessionEntry> = {
-                inputTokens: input,
-                outputTokens: output,
-                totalTokens: promptTokens > 0 ? promptTokens : (usage.total ?? input),
-                modelProvider: providerUsed,
-                model: modelUsed,
-                contextTokens: contextTokensUsed ?? entry.contextTokens,
-                systemPromptReport: runResult.meta.systemPromptReport ?? entry.systemPromptReport,
-                updatedAt: Date.now(),
-              };
-              if (cliSessionId) {
-                const nextEntry = { ...entry, ...patch };
-                setCliSessionId(nextEntry, providerUsed, cliSessionId);
-                return {
-                  ...patch,
-                  cliSessionIds: nextEntry.cliSessionIds,
-                  claudeCliSessionId: nextEntry.claudeCliSessionId,
-                };
-              }
-              return patch;
-            },
-          });
-        } catch (err) {
-          logVerbose(`failed to persist usage update: ${String(err)}`);
-        }
-      } else if (modelUsed || contextTokensUsed) {
-        try {
-          await updateSessionStoreEntry({
-            storePath,
-            sessionKey,
-            update: async (entry) => {
-              const patch: Partial<SessionEntry> = {
-                modelProvider: providerUsed ?? entry.modelProvider,
-                model: modelUsed ?? entry.model,
-                contextTokens: contextTokensUsed ?? entry.contextTokens,
-                systemPromptReport: runResult.meta.systemPromptReport ?? entry.systemPromptReport,
-                updatedAt: Date.now(),
-              };
-              if (cliSessionId) {
-                const nextEntry = { ...entry, ...patch };
-                setCliSessionId(nextEntry, providerUsed, cliSessionId);
-                return {
-                  ...patch,
-                  cliSessionIds: nextEntry.cliSessionIds,
-                  claudeCliSessionId: nextEntry.claudeCliSessionId,
-                };
-              }
-              return patch;
-            },
-          });
-        } catch (err) {
-          logVerbose(`failed to persist model/context update: ${String(err)}`);
-        }
-      }
-    }
-
     const responseUsageRaw =
       activeSessionEntry?.responseUsage ??
       (sessionKey ? activeSessionStore?.[sessionKey]?.responseUsage : undefined);
diff --git a/src/auto-reply/reply/followup-runner.test.ts b/src/auto-reply/reply/followup-runner.test.ts
index 19213081d..ceb5c2ab2 100644
--- a/src/auto-reply/reply/followup-runner.test.ts
+++ b/src/auto-reply/reply/followup-runner.test.ts
@@ -3,7 +3,7 @@ import { tmpdir } from "node:os";
 import path from "node:path";
 import { describe, expect, it, vi } from "vitest";
 
-import type { SessionEntry } from "../../config/sessions.js";
+import { loadSessionStore, saveSessionStore, type SessionEntry } from "../../config/sessions.js";
 import type { FollowupRun } from "./queue.js";
 import { createMockTypingController } from "./test-helpers.js";
 
@@ -195,4 +195,47 @@ describe("createFollowupRunner messaging tool dedupe", () => {
 
     expect(onBlockReply).not.toHaveBeenCalled();
   });
+
+  it("persists usage even when replies are suppressed", async () => {
+    const storePath = path.join(
+      await fs.mkdtemp(path.join(tmpdir(), "clawdbot-followup-usage-")),
+      "sessions.json",
+    );
+    const sessionKey = "main";
+    const sessionEntry: SessionEntry = { sessionId: "session", updatedAt: Date.now() };
+    const sessionStore: Record<string, SessionEntry> = { [sessionKey]: sessionEntry };
+    await saveSessionStore(storePath, sessionStore);
+
+    const onBlockReply = vi.fn(async () => {});
+    runEmbeddedPiAgentMock.mockResolvedValueOnce({
+      payloads: [{ text: "hello world!" }],
+      messagingToolSentTexts: ["different message"],
+      messagingToolSentTargets: [{ tool: "slack", provider: "slack", to: "channel:C1" }],
+      meta: {
+        agentMeta: {
+          usage: { input: 10, output: 5 },
+          model: "claude-opus-4-5",
+          provider: "anthropic",
+        },
+      },
+    });
+
+    const runner = createFollowupRunner({
+      opts: { onBlockReply },
+      typing: createMockTypingController(),
+      typingMode: "instant",
+      sessionEntry,
+      sessionStore,
+      sessionKey,
+      storePath,
+      defaultModel: "anthropic/claude-opus-4-5",
+    });
+
+    await runner(baseQueuedRun("slack"));
+
+    expect(onBlockReply).not.toHaveBeenCalled();
+    const store = loadSessionStore(storePath, { skipCache: true });
+    expect(store[sessionKey]?.totalTokens ?? 0).toBeGreaterThan(0);
+    expect(store[sessionKey]?.model).toBe("claude-opus-4-5");
+  });
 });
diff --git a/src/auto-reply/reply/followup-runner.ts b/src/auto-reply/reply/followup-runner.ts
index dfda65897..febbc6e6a 100644
--- a/src/auto-reply/reply/followup-runner.ts
+++ b/src/auto-reply/reply/followup-runner.ts
@@ -4,12 +4,7 @@ import { lookupContextTokens } from "../../agents/context.js";
 import { DEFAULT_CONTEXT_TOKENS } from "../../agents/defaults.js";
 import { runWithModelFallback } from "../../agents/model-fallback.js";
 import { runEmbeddedPiAgent } from "../../agents/pi-embedded.js";
-import { hasNonzeroUsage } from "../../agents/usage.js";
-import {
-  resolveAgentIdFromSessionKey,
-  type SessionEntry,
-  updateSessionStoreEntry,
-} from "../../config/sessions.js";
+import { resolveAgentIdFromSessionKey, type SessionEntry } from "../../config/sessions.js";
 import type { TypingMode } from "../../config/types.js";
 import { logVerbose } from "../../globals.js";
 import { registerAgentRunContext } from "../../infra/agent-events.js";
@@ -26,6 +21,7 @@ import {
 } from "./reply-payloads.js";
 import { resolveReplyToMode } from "./reply-threading.js";
 import { isRoutableChannel, routeReply } from "./route-reply.js";
+import { persistSessionUsageUpdate } from "./session-usage.js";
 import { incrementCompactionCount } from "./session-updates.js";
 import type { TypingController } from "./typing.js";
 import { createTypingSignaler } from "./typing-mode.js";
@@ -190,6 +186,26 @@ export function createFollowupRunner(params: {
         return;
       }
 
+      if (storePath && sessionKey) {
+        const usage = runResult.meta.agentMeta?.usage;
+        const modelUsed = runResult.meta.agentMeta?.model ?? fallbackModel ?? defaultModel;
+        const contextTokensUsed =
+          agentCfgContextTokens ??
+          lookupContextTokens(modelUsed) ??
+          sessionEntry?.contextTokens ??
+          DEFAULT_CONTEXT_TOKENS;
+
+        await persistSessionUsageUpdate({
+          storePath,
+          sessionKey,
+          usage,
+          modelUsed,
+          providerUsed: fallbackProvider,
+          contextTokensUsed,
+          logLabel: "followup",
+        });
+      }
+
       const payloadArray = runResult.payloads ?? [];
       if (payloadArray.length === 0) return;
       const sanitizedPayloads = payloadArray.flatMap((payload) => {
@@ -245,56 +261,6 @@ export function createFollowupRunner(params: {
         }
       }
 
-      if (storePath && sessionKey) {
-        const usage = runResult.meta.agentMeta?.usage;
-        const modelUsed = runResult.meta.agentMeta?.model ?? fallbackModel ?? defaultModel;
-        const contextTokensUsed =
-          agentCfgContextTokens ??
-          lookupContextTokens(modelUsed) ??
-          sessionEntry?.contextTokens ??
-          DEFAULT_CONTEXT_TOKENS;
-
-        if (hasNonzeroUsage(usage)) {
-          try {
-            await updateSessionStoreEntry({
-              storePath,
-              sessionKey,
-              update: async (entry) => {
-                const input = usage.input ?? 0;
-                const output = usage.output ?? 0;
-                const promptTokens = input + (usage.cacheRead ?? 0) + (usage.cacheWrite ?? 0);
-                return {
-                  inputTokens: input,
-                  outputTokens: output,
-                  totalTokens: promptTokens > 0 ? promptTokens : (usage.total ?? input),
-                  modelProvider: fallbackProvider ?? entry.modelProvider,
-                  model: modelUsed,
-                  contextTokens: contextTokensUsed ?? entry.contextTokens,
-                  updatedAt: Date.now(),
-                };
-              },
-            });
-          } catch (err) {
-            logVerbose(`failed to persist followup usage update: ${String(err)}`);
-          }
-        } else if (modelUsed || contextTokensUsed) {
-          try {
-            await updateSessionStoreEntry({
-              storePath,
-              sessionKey,
-              update: async (entry) => ({
-                modelProvider: fallbackProvider ?? entry.modelProvider,
-                model: modelUsed ?? entry.model,
-                contextTokens: contextTokensUsed ?? entry.contextTokens,
-                updatedAt: Date.now(),
-              }),
-            });
-          } catch (err) {
-            logVerbose(`failed to persist followup model/context update: ${String(err)}`);
-          }
-        }
-      }
-
       await sendFollowupPayloads(finalPayloads, queued);
     } finally {
       typing.markRunComplete();
diff --git a/src/auto-reply/reply/session-usage.ts b/src/auto-reply/reply/session-usage.ts
new file mode 100644
index 000000000..1a048b55e
--- /dev/null
+++ b/src/auto-reply/reply/session-usage.ts
@@ -0,0 +1,92 @@
+import { setCliSessionId } from "../../agents/cli-session.js";
+import { hasNonzeroUsage, type NormalizedUsage } from "../../agents/usage.js";
+import {
+  type SessionSystemPromptReport,
+  type SessionEntry,
+  updateSessionStoreEntry,
+} from "../../config/sessions.js";
+import { logVerbose } from "../../globals.js";
+
+export async function persistSessionUsageUpdate(params: {
+  storePath?: string;
+  sessionKey?: string;
+  usage?: NormalizedUsage;
+  modelUsed?: string;
+  providerUsed?: string;
+  contextTokensUsed?: number;
+  systemPromptReport?: SessionSystemPromptReport;
+  cliSessionId?: string;
+  logLabel?: string;
+}): Promise<void> {
+  const { storePath, sessionKey } = params;
+  if (!storePath || !sessionKey) return;
+
+  const label = params.logLabel ? `${params.logLabel} ` : "";
+  if (hasNonzeroUsage(params.usage)) {
+    try {
+      await updateSessionStoreEntry({
+        storePath,
+        sessionKey,
+        update: async (entry) => {
+          const input = params.usage?.input ?? 0;
+          const output = params.usage?.output ?? 0;
+          const promptTokens =
+            input + (params.usage?.cacheRead ?? 0) + (params.usage?.cacheWrite ?? 0);
+          const patch: Partial<SessionEntry> = {
+            inputTokens: input,
+            outputTokens: output,
+            totalTokens: promptTokens > 0 ? promptTokens : (params.usage?.total ?? input),
+            modelProvider: params.providerUsed ?? entry.modelProvider,
+            model: params.modelUsed ?? entry.model,
+            contextTokens: params.contextTokensUsed ?? entry.contextTokens,
+            systemPromptReport: params.systemPromptReport ?? entry.systemPromptReport,
+            updatedAt: Date.now(),
+          };
+          if (params.cliSessionId) {
+            const nextEntry = { ...entry, ...patch };
+            setCliSessionId(nextEntry, params.providerUsed, params.cliSessionId);
+            return {
+              ...patch,
+              cliSessionIds: nextEntry.cliSessionIds,
+              claudeCliSessionId: nextEntry.claudeCliSessionId,
+            };
+          }
+          return patch;
+        },
+      });
+    } catch (err) {
+      logVerbose(`failed to persist ${label}usage update: ${String(err)}`);
+    }
+    return;
+  }
+
+  if (params.modelUsed || params.contextTokensUsed) {
+    try {
+      await updateSessionStoreEntry({
+        storePath,
+        sessionKey,
+        update: async (entry) => {
+          const patch: Partial<SessionEntry> = {
+            modelProvider: params.providerUsed ?? entry.modelProvider,
+            model: params.modelUsed ?? entry.model,
+            contextTokens: params.contextTokensUsed ?? entry.contextTokens,
+            systemPromptReport: params.systemPromptReport ?? entry.systemPromptReport,
+            updatedAt: Date.now(),
+          };
+          if (params.cliSessionId) {
+            const nextEntry = { ...entry, ...patch };
+            setCliSessionId(nextEntry, params.providerUsed, params.cliSessionId);
+            return {
+              ...patch,
+              cliSessionIds: nextEntry.cliSessionIds,
+              claudeCliSessionId: nextEntry.claudeCliSessionId,
+            };
+          }
+          return patch;
+        },
+      });
+    } catch (err) {
+      logVerbose(`failed to persist ${label}model/context update: ${String(err)}`);
+    }
+  }
+}