diff --git a/docs/gateway/configuration.md b/docs/gateway/configuration.md
index 84676fdfe..8c4c22408 100644
--- a/docs/gateway/configuration.md
+++ b/docs/gateway/configuration.md
@@ -837,6 +837,7 @@ This is intended to reduce token usage for chatty agents that accumulate large t
 High level:
 - Never touches user/assistant messages.
 - Protects the last `keepLastAssistants` assistant messages (no tool results after that point are pruned).
+- Protects the bootstrap prefix (nothing before the first user message is pruned).
 - Modes:
   - `adaptive`: soft-trims oversized tool results (keep head/tail) when the estimated context ratio crosses `softTrimRatio`.
     Then hard-clears the oldest eligible tool results when the estimated context ratio crosses `hardClearRatio` **and**
diff --git a/src/agents/pi-extensions/context-pruning.test.ts b/src/agents/pi-extensions/context-pruning.test.ts
index 403d4735e..3d28c519e 100644
--- a/src/agents/pi-extensions/context-pruning.test.ts
+++ b/src/agents/pi-extensions/context-pruning.test.ts
@@ -141,6 +141,43 @@ describe("context-pruning", () => {
     expect(toolText(findToolResult(next, "t4"))).toContain("w".repeat(20_000));
     expect(toolText(findToolResult(next, "t1"))).toBe("[cleared]");
   });
+
+  it("never prunes tool results before the first user message", () => {
+    const settings = computeEffectiveSettings({
+      mode: "aggressive",
+      keepLastAssistants: 0,
+      hardClear: { placeholder: "[cleared]" },
+    });
+    if (!settings) throw new Error("expected settings");
+
+    const messages: AgentMessage[] = [
+      makeAssistant("bootstrap tool calls"),
+      makeToolResult({
+        toolCallId: "t0",
+        toolName: "read",
+        text: "x".repeat(20_000),
+      }),
+      makeAssistant("greeting"),
+      makeUser("u1"),
+      makeToolResult({
+        toolCallId: "t1",
+        toolName: "bash",
+        text: "y".repeat(20_000),
+      }),
+    ];
+
+    const next = pruneContextMessages({
+      messages,
+      settings,
+      ctx: { model: { contextWindow: 1000 } } as unknown as ExtensionContext,
+      isToolPrunable: () => true,
+      contextWindowTokensOverride: 1000,
+    });
+
+    expect(toolText(findToolResult(next, "t0"))).toBe("x".repeat(20_000));
+    expect(toolText(findToolResult(next, "t1"))).toBe("[cleared]");
+  });
+
   it("mode aggressive clears eligible tool results before cutoff", () => {
     const messages: AgentMessage[] = [
       makeUser("u1"),
diff --git a/src/agents/pi-extensions/context-pruning/pruner.ts b/src/agents/pi-extensions/context-pruning/pruner.ts
index 0341b2bbf..589cf1bb4 100644
--- a/src/agents/pi-extensions/context-pruning/pruner.ts
+++ b/src/agents/pi-extensions/context-pruning/pruner.ts
@@ -153,6 +153,13 @@ function findAssistantCutoffIndex(
   return null;
 }
 
+function findFirstUserIndex(messages: AgentMessage[]): number | null {
+  for (let i = 0; i < messages.length; i++) {
+    if (messages[i]?.role === "user") return i;
+  }
+  return null;
+}
+
 function softTrimToolResultMessage(params: {
   msg: ToolResultMessage;
   settings: EffectiveContextPruningSettings;
@@ -207,13 +214,20 @@ export function pruneContextMessages(params: {
   );
   if (cutoffIndex === null) return messages;
 
+  // Bootstrap safety: never prune anything before the first user message. This protects initial
+  // "identity" reads (SOUL.md, USER.md, etc.) which typically happen before the first inbound user
+  // message exists in the session transcript.
+  const firstUserIndex = findFirstUserIndex(messages);
+  const pruneStartIndex =
+    firstUserIndex === null ? messages.length : firstUserIndex;
+
   const isToolPrunable =
     params.isToolPrunable ?? makeToolPrunablePredicate(settings.tools);
 
   if (settings.mode === "aggressive") {
     let next: AgentMessage[] | null = null;
 
-    for (let i = 0; i < cutoffIndex; i++) {
+    for (let i = pruneStartIndex; i < cutoffIndex; i++) {
       const msg = messages[i];
       if (!msg || msg.role !== "toolResult") continue;
       if (!isToolPrunable(msg.toolName)) continue;
@@ -248,7 +262,7 @@ export function pruneContextMessages(params: {
   const prunableToolIndexes: number[] = [];
   let next: AgentMessage[] | null = null;
 
-  for (let i = 0; i < cutoffIndex; i++) {
+  for (let i = pruneStartIndex; i < cutoffIndex; i++) {
     const msg = messages[i];
     if (!msg || msg.role !== "toolResult") continue;
     if (!isToolPrunable(msg.toolName)) continue;