diff --git a/src/peft/tuners/tuners_utils.py b/src/peft/tuners/tuners_utils.py
index a94fe4f2e2..cc44684d80 100644
--- a/src/peft/tuners/tuners_utils.py
+++ b/src/peft/tuners/tuners_utils.py
@@ -1722,12 +1722,20 @@ def check_target_module_exists(config, key: str) -> bool | re.Match[str] | None:
             # TODO: It's still unclear how empty layers_pattern (None, [], or "") should behave
             # For now, empty layers_pattern means any layer pattern is ok
             if layers_pattern is None or len(layers_pattern) == 0:
-                layer_index = re.match(r".*\.[^.]*\.(\d+)\.", key)
+                layer_index = re.search(r"(?:^|\.)[^.]*\.(\d+)\.", key)
+                # Avoid treating expert index as "layer index" in MoE module paths like "...experts.<i>...."
+                if layer_index is not None and key[layer_index.start() :].startswith(".experts."):
+                    layer_index = None
             else:
                 layers_pattern = [layers_pattern] if isinstance(layers_pattern, str) else layers_pattern
+                layer_index = None
                 for pattern in layers_pattern:
-                    layer_index = re.match(rf".*\.{pattern}\.(\d+)\.", key)
-                    if layer_index is not None:
+                    m = re.search(rf"(?:^|\.){pattern}\.(\d+)\.", key)
+                    # Avoid treating expert index as "layer index" in MoE module paths like "...experts.<i>...."
+                    if m is not None and key[m.start() :].startswith(".experts."):
+                        continue
+                    if m is not None:
+                        layer_index = m
                         break
 
             if layer_index is None:
diff --git a/tests/test_layers_to_transform_moe.py b/tests/test_layers_to_transform_moe.py
new file mode 100644
index 0000000000..2423ee0587
--- /dev/null
+++ b/tests/test_layers_to_transform_moe.py
@@ -0,0 +1,45 @@
+from torch import nn
+
+from peft import LoraConfig, get_peft_model
+
+
+def test_layers_to_transform_filters_by_layer_not_expert_index():
+    class ToyMoEBlock(nn.Module):
+        def __init__(self):
+            super().__init__()
+            self.self_attn = nn.Module()
+            self.self_attn.q_proj = nn.Linear(4, 4, bias=False)
+
+            self.mlp = nn.Module()
+            self.mlp.experts = nn.ModuleList([nn.Module() for _ in range(2)])
+            for e in range(2):
+                self.mlp.experts[e].up_proj = nn.Linear(4, 4, bias=False)
+
+        def forward(self, x):
+            return x
+
+    class ToyMoEModel(nn.Module):
+        def __init__(self):
+            super().__init__()
+            self.model = nn.Module()
+            self.model.layers = nn.ModuleList([ToyMoEBlock() for _ in range(4)])
+
+        def forward(self, x):
+            return x
+
+    model = ToyMoEModel()
+
+    config = LoraConfig(
+        target_modules=["q_proj", "up_proj"],
+        # layers_pattern="layers",
+        layers_to_transform=[1],
+        r=2,
+        lora_alpha=4,
+    )
+    model = get_peft_model(model, config)
+    targeted = set(model.targeted_module_names)
+
+    assert "model.layers.1.self_attn.q_proj" in targeted
+    assert "model.layers.1.mlp.experts.0.up_proj" in targeted
+    assert "model.layers.1.mlp.experts.1.up_proj" in targeted
+    assert "model.layers.2.mlp.experts.1.up_proj" not in targeted  # must not match by expert index