diff --git a/pyiceberg/table/__init__.py b/pyiceberg/table/__init__.py
index c0adce84dc..0faacae27d 100644
--- a/pyiceberg/table/__init__.py
+++ b/pyiceberg/table/__init__.py
@@ -362,7 +362,7 @@ def _set_ref_snapshot(
         return updates, requirements
 
     def _build_partition_predicate(
-        self, partition_records: set[Record], spec: PartitionSpec, schema: Schema
+        self, partition_records: set[Record], spec: PartitionSpec, schema: Schema, is_projected: bool = False
     ) -> BooleanExpression:
         """Build a filter predicate matching any of the input partition records.
 
@@ -370,10 +370,13 @@ def _build_partition_predicate(
             partition_records: A set of partition records to match
             spec: An optional partition spec, if none then defaults to current
             schema: An optional schema, if none then defaults to current
+            is_projected: Reference the partition fields rather than their source columns.
+
         Returns:
             A predicate matching any of the input partition records.
         """
-        partition_fields = [schema.find_field(field.source_id).name for field in spec.fields]
+        partition_fields = [(field.name if is_projected else schema.find_field(field.source_id).name) for field in spec.fields]
+
         if not partition_records or not partition_fields:
             return AlwaysFalse()
 
diff --git a/pyiceberg/table/update/snapshot.py b/pyiceberg/table/update/snapshot.py
index 7931edacdd..9285c98bd6 100644
--- a/pyiceberg/table/update/snapshot.py
+++ b/pyiceberg/table/update/snapshot.py
@@ -381,10 +381,14 @@ def _build_delete_files_partition_predicate(self) -> None:
             group.add(data_file.partition)
 
         for spec_id, partition_records in partition_to_overwrite.items():
-            self.delete_by_predicate(
+            self.partition_filters[spec_id] = Or(
+                self.partition_filters[spec_id],
                 self._transaction._build_partition_predicate(
-                    partition_records=partition_records, schema=self.schema(), spec=self.spec(spec_id)
-                )
+                    partition_records=partition_records,
+                    schema=self.schema(),
+                    spec=self.spec(spec_id),
+                    is_projected=True,
+                ),
             )
 
 
diff --git a/tests/table/test_upsert.py b/tests/table/test_upsert.py
index 08f90c6600..78ddbc7c5c 100644
--- a/tests/table/test_upsert.py
+++ b/tests/table/test_upsert.py
@@ -14,6 +14,7 @@
 # KIND, either express or implied.  See the License for the
 # specific language governing permissions and limitations
 # under the License.
+from datetime import datetime
 from pathlib import PosixPath
 
 import pyarrow as pa
@@ -26,11 +27,13 @@
 from pyiceberg.expressions import AlwaysTrue, And, EqualTo, Reference
 from pyiceberg.expressions.literals import LongLiteral
 from pyiceberg.io.pyarrow import schema_to_pyarrow
+from pyiceberg.partitioning import PartitionField, PartitionSpec
 from pyiceberg.schema import Schema
 from pyiceberg.table import Table, UpsertResult
 from pyiceberg.table.snapshots import Operation
 from pyiceberg.table.upsert_util import create_match_filter
-from pyiceberg.types import IntegerType, NestedField, StringType, StructType
+from pyiceberg.transforms import DayTransform
+from pyiceberg.types import IntegerType, NestedField, StringType, StructType, TimestampType
 from tests.catalog.test_base import InMemoryCatalog
 
 
@@ -714,6 +717,42 @@ def test_upsert_with_nulls(catalog: Catalog) -> None:
     )
 
 
+def test_upsert_on_table_partitioned_by_transform(catalog: Catalog) -> None:
+    """Upsert has to rewrite the matched file on a table partitioned by a non-identity transform.
+
+    The manifest pruning in the overwrite builds its predicate from the partition records of
+    the deleted files. Those records hold already-transformed values, so referencing the source
+    column would send them through the transform twice, prune away the only relevant manifest
+    and leave the replaced row behind as a duplicate.
+    """
+    identifier = "default.test_upsert_on_table_partitioned_by_transform"
+    _drop_table(catalog, identifier)
+
+    schema = Schema(
+        NestedField(1, "k", StringType(), required=False),
+        NestedField(2, "v", IntegerType(), required=False),
+        NestedField(3, "ts", TimestampType(), required=False),
+    )
+    spec = PartitionSpec(PartitionField(source_id=3, field_id=1000, transform=DayTransform(), name="ts_day"))
+    table = catalog.create_table(identifier, schema, partition_spec=spec)
+
+    arrow_schema = schema_to_pyarrow(schema)
+    # A timestamp whose day ordinal is far from the value it would be read as if the
+    # DayTransform were applied a second time.
+    ts = datetime(2026, 1, 6, 12)
+
+    def rows(pairs: list[tuple[str, int]]) -> pa_table:
+        return pa.Table.from_pylist([{"k": k, "v": v, "ts": ts} for k, v in pairs], schema=arrow_schema)
+
+    table.append(rows([("a", 1), ("b", 1)]))
+
+    res = table.upsert(rows([("a", 2)]), join_cols=["k"])
+    assert_upsert_result(res, expected_updated=1, expected_inserted=0)
+
+    arrow = table.scan().to_arrow()
+    assert sorted(zip(arrow["k"].to_pylist(), arrow["v"].to_pylist(), strict=True)) == [("a", 2), ("b", 1)]
+
+
 def test_transaction(catalog: Catalog) -> None:
     """Test the upsert within a Transaction. Make sure that if something fails the entire Transaction is
     rolled back."""