diff --git a/src/passes/InstrumentBranchHints.cpp b/src/passes/InstrumentBranchHints.cpp
index 656397a5ad1..0fa6f3009b6 100644
--- a/src/passes/InstrumentBranchHints.cpp
+++ b/src/passes/InstrumentBranchHints.cpp
@@ -96,6 +96,7 @@
 //
 
 #include "ir/drop.h"
+#include "ir/effects.h"
 #include "ir/eh-utils.h"
 #include "ir/find_all.h"
 #include "ir/local-graph.h"
@@ -272,6 +273,8 @@ struct InstrumentationProcessor : public WalkerPass<PostWalker<Sub>> {
     // The condition before the instrumentation (a pointer to it, so we can
     // replace it).
     Expression** originalCondition;
+    // The local that the original condition is stored in temporarily.
+    Index tempLocal;
     // The call to the logging that the instrumentation added.
     Call* call;
   };
@@ -330,7 +333,7 @@ struct InstrumentationProcessor : public WalkerPass<PostWalker<Sub>> {
       return {};
     }
     // Great, this is indeed a prior instrumentation.
-    return Instrumentation{&set->value, call};
+    return Instrumentation{&set->value, set->index, call};
   }
 };
 
@@ -374,7 +377,27 @@ struct DeInstrumentBranchHints
       // IR, and the original condition is still used in another place, until
       // we remove the logging calls; since we will remove the calls anyhow, we
       // just need some valid IR there).
-      std::swap(curr->condition, *info->originalCondition);
+      //
+      // Check for dangerous effects in the condition we are about to replace,
+      // to avoid a situation where the condition looks like this:
+      //
+      //  (set $temp (original condition))
+      //   ..effects..
+      //  (local.get $temp)
+      //
+      // We cannot replace all this with the original condition, as it would
+      // remove the effects. (Even in that case we will remove the actual call
+      // to log the branch hint, below, so this just prevents some cleanup that
+      // is normally safe - the cleanup is mainly useful to allow inspection of
+      // testcases for debugging.)
+      EffectAnalyzer effects(getPassOptions(), *getModule(), curr->condition);
+      // The only condition we allow is a write to the temp local from the
+      // instrumentation, which getInstrumentation() verified has no other uses
+      // than us.
+      effects.localsWritten.erase(info->tempLocal);
+      if (!effects.hasUnremovableSideEffects()) {
+        std::swap(curr->condition, *info->originalCondition);
+      }
     }
   }
 
@@ -403,6 +426,21 @@ struct DeInstrumentBranchHints
       }
     }
   }
+
+  void doWalkModule(Module* module) {
+    auto logBranchImport = getLogBranchImport(module);
+    if (!logBranchImport) {
+      Fatal()
+        << "No branch hint logging import found. Was this code instrumented?";
+    }
+
+    // Mark the log-branch import as having no side effects - we are removing it
+    // entirely here, and its effect should not stop us when we compute effects.
+    module->getFunction(logBranchImport)->effects =
+      std::make_shared<EffectAnalyzer>(getPassOptions(), *module);
+
+    InstrumentationProcessor<DeInstrumentBranchHints>::doWalkModule(module);
+  }
 };
 
 } // anonymous namespace
diff --git a/test/lit/passes/deinstrument-branch-hints.wast b/test/lit/passes/deinstrument-branch-hints.wast
index 6d619c4b28b..3f9019028e7 100644
--- a/test/lit/passes/deinstrument-branch-hints.wast
+++ b/test/lit/passes/deinstrument-branch-hints.wast
@@ -7,6 +7,8 @@
 
   ;; CHECK:      (type $1 (func (param i32 i32 i32)))
 
+  ;; CHECK:      (type $2 (func (result i32)))
+
   ;; CHECK:      (import "fuzzing-support" "log-branch" (func $log (type $1) (param i32 i32 i32)))
   (import "fuzzing-support" "log-branch" (func $log (param i32 i32 i32)))
 
@@ -164,4 +166,57 @@
       )
     )
   )
+
+  ;; CHECK:      (func $if-unreachable (type $2) (result i32)
+  ;; CHECK-NEXT:  (local $0 i32)
+  ;; CHECK-NEXT:  (block $block (result i32)
+  ;; CHECK-NEXT:   (br_if $block
+  ;; CHECK-NEXT:    (i32.const 0)
+  ;; CHECK-NEXT:    (block (result i32)
+  ;; CHECK-NEXT:     (block
+  ;; CHECK-NEXT:      (local.set $0
+  ;; CHECK-NEXT:       (i32.const 42)
+  ;; CHECK-NEXT:      )
+  ;; CHECK-NEXT:      (if
+  ;; CHECK-NEXT:       (i32.const 1)
+  ;; CHECK-NEXT:       (then
+  ;; CHECK-NEXT:        (unreachable)
+  ;; CHECK-NEXT:       )
+  ;; CHECK-NEXT:      )
+  ;; CHECK-NEXT:     )
+  ;; CHECK-NEXT:     (nop)
+  ;; CHECK-NEXT:     (local.get $0)
+  ;; CHECK-NEXT:    )
+  ;; CHECK-NEXT:   )
+  ;; CHECK-NEXT:  )
+  ;; CHECK-NEXT: )
+  (func $if-unreachable (result i32)
+    (local $0 i32)
+    ;; The unreachable here must be executed. Normally we replace the br_if's
+    ;; entire condition, but here we only remove the call to $log.
+    (block $block (result i32)
+      (br_if $block
+        (i32.const 0)
+        (block (result i32)
+          (block
+            (local.set $0
+              (i32.const 42)
+            )
+            (if
+              (i32.const 1)
+              (then
+                (unreachable)
+              )
+            )
+          )
+          (call $log
+            (i32.const 0)
+            (i32.const 0)
+            (local.get $0)
+          )
+          (local.get $0)
+        )
+      )
+    )
+  )
 )