diff --git a/sdks/java/io/iceberg/src/main/java/org/apache/beam/sdk/io/iceberg/IcebergScanConfig.java b/sdks/java/io/iceberg/src/main/java/org/apache/beam/sdk/io/iceberg/IcebergScanConfig.java
index 3829baa43665..c1a324ad844c 100644
--- a/sdks/java/io/iceberg/src/main/java/org/apache/beam/sdk/io/iceberg/IcebergScanConfig.java
+++ b/sdks/java/io/iceberg/src/main/java/org/apache/beam/sdk/io/iceberg/IcebergScanConfig.java
@@ -26,7 +26,6 @@
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
-import java.util.stream.Collectors;
 import org.apache.beam.sdk.io.iceberg.IcebergIO.ReadRows.StartingStrategy;
 import org.apache.beam.sdk.schemas.Schema;
 import org.apache.beam.vendor.guava.v32_1_2_jre.com.google.common.annotations.VisibleForTesting;
@@ -37,7 +36,6 @@
 import org.apache.iceberg.catalog.TableIdentifier;
 import org.apache.iceberg.expressions.Evaluator;
 import org.apache.iceberg.expressions.Expression;
-import org.apache.iceberg.types.Types;
 import org.checkerframework.checker.nullness.qual.MonotonicNonNull;
 import org.checkerframework.checker.nullness.qual.Nullable;
 import org.checkerframework.dataflow.qual.Pure;
@@ -93,10 +91,30 @@ static org.apache.iceberg.Schema resolveSchema(
     if (keep != null && !keep.isEmpty()) {
       selectedFieldsBuilder.addAll(keep);
     } else if (drop != null && !drop.isEmpty()) {
-      Set<String> fields =
-          schema.columns().stream().map(Types.NestedField::name).collect(Collectors.toSet());
-      drop.forEach(fields::remove);
-      selectedFieldsBuilder.addAll(fields);
+      // Get all field paths including nested ones
+      java.util.List<String> allPaths =
+          new java.util.ArrayList<>(
+              org.apache.iceberg.types.TypeUtil.indexByName(schema.asStruct()).keySet());
+      java.util.Collections.sort(allPaths);
+
+      // Identify leaf fields only (fields that are not parents of other fields)
+      // This prevents selecting a parent struct from implicitly including dropped children
+      java.util.Set<String> leaves = new java.util.HashSet<>();
+      for (int i = 0; i < allPaths.size(); i++) {
+        String path = allPaths.get(i);
+        // If the next path starts with "path.", then "path" is a parent - skip it
+        if (i + 1 < allPaths.size() && allPaths.get(i + 1).startsWith(path + ".")) {
+          continue;
+        }
+        leaves.add(path);
+      }
+
+      // Remove fields that are dropped or are children of dropped fields
+      for (String d : drop) {
+        leaves.removeIf(f -> f.equals(d) || f.startsWith(d + "."));
+      }
+
+      selectedFieldsBuilder.addAll(leaves);
     } else {
       // default: include all columns
       return schema;
@@ -327,7 +345,9 @@ void validate(Table table) {
         param = "drop";
         fieldsSpecified = newHashSet(checkNotNull(drop));
       }
-      table.schema().columns().forEach(nf -> fieldsSpecified.remove(nf.name()));
+      // Use findField() to support nested column paths (e.g., "colA.colB")
+      // Iceberg's Schema.findField() resolves dot-notation paths for nested fields
+      fieldsSpecified.removeIf(name -> table.schema().findField(name) != null);
 
       checkArgument(
           fieldsSpecified.isEmpty(),
diff --git a/sdks/java/io/iceberg/src/test/java/org/apache/beam/sdk/io/iceberg/IcebergIOReadTest.java b/sdks/java/io/iceberg/src/test/java/org/apache/beam/sdk/io/iceberg/IcebergIOReadTest.java
index bb303ea9c305..8b1037168037 100644
--- a/sdks/java/io/iceberg/src/test/java/org/apache/beam/sdk/io/iceberg/IcebergIOReadTest.java
+++ b/sdks/java/io/iceberg/src/test/java/org/apache/beam/sdk/io/iceberg/IcebergIOReadTest.java
@@ -273,6 +273,53 @@ public void testProjectedSchema() {
     assertTrue(projectKeep.sameSchema(expectedKeep));
   }
 
+  @Test
+  public void testNestedColumnPruningValidation() {
+    // Test that nested column paths (dot notation) are accepted in keep/drop configuration
+    org.apache.iceberg.Schema schemaWithNested =
+        new org.apache.iceberg.Schema(
+            required(1, "id", StringType.get()),
+            required(
+                2,
+                "data",
+                StructType.of(
+                    required(3, "name", StringType.get()), required(4, "value", StringType.get()))),
+            required(5, "metadata", StringType.get()));
+
+    // Test that nested column path "data.name" is valid and can be selected
+    org.apache.iceberg.Schema projectNestedKeep =
+        resolveSchema(schemaWithNested, asList("id", "data.name"), null);
+
+    // Verify the projected schema contains the nested field
+    assertTrue(projectNestedKeep.findField("id") != null);
+    assertTrue(projectNestedKeep.findField("data.name") != null);
+  }
+
+  @Test
+  public void testNestedColumnDropValidation() {
+    // Test that nested column paths work correctly with drop configuration
+    org.apache.iceberg.Schema schemaWithNested =
+        new org.apache.iceberg.Schema(
+            required(1, "id", StringType.get()),
+            required(
+                2,
+                "data",
+                StructType.of(
+                    required(3, "name", StringType.get()), required(4, "value", StringType.get()))),
+            required(5, "metadata", StringType.get()));
+
+    // Test dropping a nested field "data.name" - should keep id, data.value, metadata
+    org.apache.iceberg.Schema projectNestedDrop =
+        resolveSchema(schemaWithNested, null, asList("data.name"));
+
+    // Verify "data.name" is NOT in the projected schema
+    assertTrue(projectNestedDrop.findField("id") != null);
+    assertTrue(projectNestedDrop.findField("data.value") != null);
+    assertTrue(projectNestedDrop.findField("metadata") != null);
+    // data.name should be dropped
+    assertTrue(projectNestedDrop.findField("data.name") == null);
+  }
+
   @Test
   public void testSimpleScan() throws Exception {
     TableIdentifier tableId =