diff --git a/.changeset/fix-prune-messages-caller-deps.md b/.changeset/fix-prune-messages-caller-deps.md
new file mode 100644
index 000000000000..0682276e9ea3
--- /dev/null
+++ b/.changeset/fix-prune-messages-caller-deps.md
@@ -0,0 +1,5 @@
+---
+'ai': patch
+---
+
+Fix `pruneMessages` dropping tool calls referenced via provider-specific caller dependencies (e.g. Anthropic `code_execution` `caller.toolId`), causing "source tool not found" API errors.
diff --git a/packages/ai/src/generate-text/prune-messages.test.ts b/packages/ai/src/generate-text/prune-messages.test.ts
index 49d52b4c4d64..8b3db5e7edc4 100644
--- a/packages/ai/src/generate-text/prune-messages.test.ts
+++ b/packages/ai/src/generate-text/prune-messages.test.ts
@@ -716,5 +716,114 @@ describe('pruneMessages', () => {
         `);
       });
     });
+
+    describe('caller tool id dependencies', () => {
+      it('should keep referenced caller tool calls when pruning', () => {
+        const messages: ModelMessage[] = [
+          {
+            role: 'user',
+            content: [{ type: 'text', text: 'Use code execution.' }],
+          },
+          // server_tool_use (provider-executed)
+          {
+            role: 'assistant',
+            content: [
+              {
+                type: 'tool-call',
+                toolCallId: 'srvtoolu_ABC',
+                toolName: 'code_execution',
+                input: {},
+                providerExecuted: true,
+              },
+            ],
+          },
+          {
+            role: 'tool',
+            content: [
+              {
+                type: 'tool-result',
+                toolCallId: 'srvtoolu_ABC',
+                toolName: 'code_execution',
+                output: { type: 'text', value: 'executed' },
+              },
+            ],
+          },
+          // programmatic tool_use referencing the server_tool_use via caller
+          {
+            role: 'assistant',
+            content: [
+              {
+                type: 'tool-call',
+                toolCallId: 'toolu_XYZ',
+                toolName: 'lookup',
+                input: { ticker: 'AAPL' },
+                providerOptions: {
+                  anthropic: {
+                    caller: {
+                      type: 'code_execution_20250825',
+                      toolId: 'srvtoolu_ABC',
+                    },
+                  },
+                },
+              },
+            ],
+          },
+          {
+            role: 'tool',
+            content: [
+              {
+                type: 'tool-result',
+                toolCallId: 'toolu_XYZ',
+                toolName: 'lookup',
+                output: { type: 'text', value: '185.42' },
+              },
+            ],
+          },
+          // final assistant text
+          {
+            role: 'assistant',
+            content: [{ type: 'text', text: 'AAPL is $185.42.' }],
+          },
+          // follow-up turn
+          {
+            role: 'user',
+            content: [{ type: 'text', text: 'Now check MSFT.' }],
+          },
+        ];
+
+        const result = pruneMessages({
+          messages,
+          toolCalls: 'before-last-5-messages',
+          emptyMessages: 'remove',
+        });
+
+        // srvtoolu_ABC must be kept because toolu_XYZ references it via caller
+        const allToolCallIds = result.flatMap(m =>
+          typeof m.content === 'string'
+            ? []
+            : m.content
+                .filter(
+                  (p): p is { type: 'tool-call'; toolCallId: string } =>
+                    p.type === 'tool-call',
+                )
+                .map(p => p.toolCallId),
+        );
+        const allToolResultIds = result.flatMap(m =>
+          typeof m.content === 'string'
+            ? []
+            : m.content
+                .filter(
+                  (p): p is { type: 'tool-result'; toolCallId: string } =>
+                    p.type === 'tool-result',
+                )
+                .map(p => p.toolCallId),
+        );
+
+        expect(allToolCallIds).toContain('srvtoolu_ABC');
+        expect(allToolCallIds).toContain('toolu_XYZ');
+        expect(allToolResultIds).toContain('srvtoolu_ABC');
+        expect(allToolResultIds).toContain('toolu_XYZ');
+      });
+    });
   });
 });
diff --git a/packages/ai/src/generate-text/prune-messages.ts b/packages/ai/src/generate-text/prune-messages.ts
index 953cc3ea7211..0f0961597c57 100644
--- a/packages/ai/src/generate-text/prune-messages.ts
+++ b/packages/ai/src/generate-text/prune-messages.ts
@@ -98,6 +98,35 @@ export function pruneMessages({
           }
         }
       }
+
+      // Transitively keep tool calls referenced via provider-specific
+      // caller dependencies (e.g. Anthropic's code_execution caller.toolId).
+      let previousSize = 0;
+      while (keptToolCallIds.size !== previousSize) {
+        previousSize = keptToolCallIds.size;
+        for (const message of messages) {
+          if (
+            message.role === 'assistant' &&
+            typeof message.content !== 'string'
+          ) {
+            for (const part of message.content) {
+              if (
+                part.type === 'tool-call' &&
+                keptToolCallIds.has(part.toolCallId)
+              ) {
+                const callerToolId = (
+                  part.providerOptions?.anthropic as
+                    | { caller?: { toolId?: string } }
+                    | undefined
+                )?.caller?.toolId;
+                if (callerToolId) {
+                  keptToolCallIds.add(callerToolId);
+                }
+              }
+            }
+          }
+        }
+      }
     }
 
     messages = messages.map((message, messageIndex) => {