diff --git a/x-pack/plugin/core/src/main/java/org/elasticsearch/xpack/core/transform/transforms/pivot/PivotConfig.java b/x-pack/plugin/core/src/main/java/org/elasticsearch/xpack/core/transform/transforms/pivot/PivotConfig.java
index e5225cb4ab9..c4e8636f155 100644
--- a/x-pack/plugin/core/src/main/java/org/elasticsearch/xpack/core/transform/transforms/pivot/PivotConfig.java
+++ b/x-pack/plugin/core/src/main/java/org/elasticsearch/xpack/core/transform/transforms/pivot/PivotConfig.java
@@ -197,9 +197,8 @@ public class PivotConfig implements Writeable, ToXContentObject {
             return Collections.emptyList();
         }
         List<String> usedNames = new ArrayList<>();
-        // TODO this will need to change once we allow multi-bucket aggs + field merging
-        aggregationConfig.getAggregatorFactories().forEach(agg -> addAggNames(agg, usedNames));
-        aggregationConfig.getPipelineAggregatorFactories().forEach(agg -> addAggNames(agg, usedNames));
+        aggregationConfig.getAggregatorFactories().forEach(agg -> addAggNames("", agg, usedNames));
+        aggregationConfig.getPipelineAggregatorFactories().forEach(agg -> addAggNames("", agg, usedNames));
         usedNames.addAll(groups.getGroups().keySet());
         return aggFieldValidation(usedNames);
     }
@@ -251,13 +250,18 @@ public class PivotConfig implements Writeable, ToXContentObject {
         return validationFailures;
     }
 
-    private static void addAggNames(AggregationBuilder aggregationBuilder, Collection<String> names) {
-        names.add(aggregationBuilder.getName());
-        aggregationBuilder.getSubAggregations().forEach(agg -> addAggNames(agg, names));
-        aggregationBuilder.getPipelineAggregations().forEach(agg -> addAggNames(agg, names));
+    private static void addAggNames(String namePrefix, AggregationBuilder aggregationBuilder, Collection<String> names) {
+        if (aggregationBuilder.getSubAggregations().isEmpty() && aggregationBuilder.getPipelineAggregations().isEmpty()) {
+            names.add(namePrefix + aggregationBuilder.getName());
+            return;
+        }
+
+        String newNamePrefix = namePrefix + aggregationBuilder.getName() + ".";
+        aggregationBuilder.getSubAggregations().forEach(agg -> addAggNames(newNamePrefix, agg, names));
+        aggregationBuilder.getPipelineAggregations().forEach(agg -> addAggNames(newNamePrefix, agg, names));
     }
 
-    private static void addAggNames(PipelineAggregationBuilder pipelineAggregationBuilder, Collection<String> names) {
-        names.add(pipelineAggregationBuilder.getName());
+    private static void addAggNames(String namePrefix, PipelineAggregationBuilder pipelineAggregationBuilder, Collection<String> names) {
+        names.add(namePrefix + pipelineAggregationBuilder.getName());
     }
 }
diff --git a/x-pack/plugin/core/src/test/java/org/elasticsearch/xpack/core/transform/transforms/pivot/PivotConfigTests.java b/x-pack/plugin/core/src/test/java/org/elasticsearch/xpack/core/transform/transforms/pivot/PivotConfigTests.java
index fa69ba55638..2d97410ce45 100644
--- a/x-pack/plugin/core/src/test/java/org/elasticsearch/xpack/core/transform/transforms/pivot/PivotConfigTests.java
+++ b/x-pack/plugin/core/src/test/java/org/elasticsearch/xpack/core/transform/transforms/pivot/PivotConfigTests.java
@@ -158,6 +158,28 @@ public class PivotConfigTests extends AbstractSerializingTransformTestCase<Pivot
         expectThrows(IllegalArgumentException.class, () -> createPivotConfigFromString(pivot, false));
     }
 
+    public void testAggDuplicates() throws IOException {
+        String pivot = "{"
+            + " \"group_by\": {"
+            + "   \"id\": {"
+            + "     \"terms\": {"
+            + "       \"field\": \"id\""
+            + "} } },"
+            + " \"aggs\": {"
+            + "   \"points\": {"
+            + "     \"max\": {"
+            + "       \"field\": \"points\""
+            + "} },"
+            + "   \"points\": {"
+            + "     \"min\": {"
+            + "       \"field\": \"points\""
+            + "} } }"
+            + "}";
+
+        // this throws early in the agg framework
+        expectThrows(IllegalArgumentException.class, () -> createPivotConfigFromString(pivot, false));
+    }
+
     public void testValidAggNames() throws IOException {
         String pivotAggs = "{"
             + " \"group_by\": {"
@@ -176,6 +198,182 @@ public class PivotConfigTests extends AbstractSerializingTransformTestCase<Pivot
         assertTrue(fieldValidation.isEmpty());
     }
 
+    public void testValidAggNamesNested() throws IOException {
+        String pivotAggs = "{"
+            + "\"group_by\": {"
+            + "  \"timestamp\": {"
+            + "    \"date_histogram\": {"
+            + "      \"field\": \"timestamp\","
+            + "      \"fixed_interval\": \"1d\""
+            + "    }"
+            + "  }"
+            + "},"
+            + "\"aggregations\": {"
+            + "  \"jp\": {"
+            + "    \"filter\": {"
+            + "      \"term\": {"
+            + "        \"geo.src\": \"JP\""
+            + "      }"
+            + "    },"
+            + "    \"aggs\": {"
+            + "      \"os.dc\": {"
+            + "        \"cardinality\": {"
+            + "          \"field\": \"machine.os.keyword\""
+            + "        }"
+            + "      }"
+            + "    }"
+            + "  },"
+            + "  \"us\": {"
+            + "    \"filter\": {"
+            + "      \"term\": {"
+            + "        \"geo.src\": \"US\""
+            + "      }"
+            + "    },"
+            + "    \"aggs\": {"
+            + "      \"os.dc\": {"
+            + "        \"cardinality\": {"
+            + "          \"field\": \"machine.os.keyword\""
+            + "} } } } } }";
+
+        PivotConfig pivotConfig = createPivotConfigFromString(pivotAggs, true);
+        assertTrue(pivotConfig.isValid());
+        List<String> fieldValidation = pivotConfig.aggFieldValidation();
+        assertTrue(Strings.collectionToCommaDelimitedString(fieldValidation), fieldValidation.isEmpty());
+    }
+
+    public void testValidAggNamesNestedTwice() throws IOException {
+        String pivotAggs = "{"
+            + "    \"group_by\": {"
+            + "      \"timestamp\": {"
+            + "        \"date_histogram\": {"
+            + "          \"field\": \"timestamp\","
+            + "          \"fixed_interval\": \"1d\""
+            + "        }"
+            + "      }"
+            + "    },"
+            + "    \"aggregations\": {"
+            + "      \"jp\": {"
+            + "        \"filter\": {"
+            + "          \"term\": {"
+            + "            \"geo.src\": \"JP\""
+            + "          }"
+            + "        },"
+            + "        \"aggs\": {"
+            + "          \"us\": {"
+            + "            \"filter\": {"
+            + "              \"term\": {"
+            + "                \"geo.dest\": \"US\""
+            + "              }"
+            + "            },"
+            + "            \"aggs\": {"
+            + "              \"os.dc\": {"
+            + "                \"cardinality\": {"
+            + "                  \"field\": \"machine.os.keyword\""
+            + "                }"
+            + "              }"
+            + "            }"
+            + "          }"
+            + "        }"
+            + "      },"
+            + "      \"us\": {"
+            + "        \"filter\": {"
+            + "          \"term\": {"
+            + "            \"geo.src\": \"US\""
+            + "          }"
+            + "        },"
+            + "        \"aggs\": {"
+            + "          \"jp\": {"
+            + "            \"filter\": {"
+            + "              \"term\": {"
+            + "                \"geo.dest\": \"JP\""
+            + "              }"
+            + "            },"
+            + "            \"aggs\": {"
+            + "              \"os.dc\": {"
+            + "                \"cardinality\": {"
+            + "                  \"field\": \"machine.os.keyword\""
+            + "                }"
+            + "              }"
+            + "            }"
+            + "          }"
+            + "        }"
+            + "      }"
+            + "    }"
+            + "  }";
+
+        PivotConfig pivotConfig = createPivotConfigFromString(pivotAggs, true);
+        assertTrue(pivotConfig.isValid());
+        List<String> fieldValidation = pivotConfig.aggFieldValidation();
+        assertTrue(Strings.collectionToCommaDelimitedString(fieldValidation), fieldValidation.isEmpty());
+    }
+
+    public void testInValidAggNamesNestedTwice() throws IOException {
+        String pivotAggs = "{"
+            + "    \"group_by\": {"
+            + "      \"jp.us.os.dc\": {"
+            + "        \"date_histogram\": {"
+            + "          \"field\": \"timestamp\","
+            + "          \"fixed_interval\": \"1d\""
+            + "        }"
+            + "      }"
+            + "    },"
+            + "    \"aggregations\": {"
+            + "      \"jp\": {"
+            + "        \"filter\": {"
+            + "          \"term\": {"
+            + "            \"geo.src\": \"JP\""
+            + "          }"
+            + "        },"
+            + "        \"aggs\": {"
+            + "          \"us\": {"
+            + "            \"filter\": {"
+            + "              \"term\": {"
+            + "                \"geo.dest\": \"US\""
+            + "              }"
+            + "            },"
+            + "            \"aggs\": {"
+            + "              \"os.dc\": {"
+            + "                \"cardinality\": {"
+            + "                  \"field\": \"machine.os.keyword\""
+            + "                }"
+            + "              }"
+            + "            }"
+            + "          }"
+            + "        }"
+            + "      },"
+            + "      \"us\": {"
+            + "        \"filter\": {"
+            + "          \"term\": {"
+            + "            \"geo.src\": \"US\""
+            + "          }"
+            + "        },"
+            + "        \"aggs\": {"
+            + "          \"jp\": {"
+            + "            \"filter\": {"
+            + "              \"term\": {"
+            + "                \"geo.dest\": \"JP\""
+            + "              }"
+            + "            },"
+            + "            \"aggs\": {"
+            + "              \"os.dc\": {"
+            + "                \"cardinality\": {"
+            + "                  \"field\": \"machine.os.keyword\""
+            + "                }"
+            + "              }"
+            + "            }"
+            + "          }"
+            + "        }"
+            + "      }"
+            + "    }"
+            + "  }";
+
+        PivotConfig pivotConfig = createPivotConfigFromString(pivotAggs, true);
+        assertTrue(pivotConfig.isValid());
+        List<String> fieldValidation = pivotConfig.aggFieldValidation();
+
+        assertThat(fieldValidation, containsInAnyOrder("duplicate field [jp.us.os.dc] detected"));
+    }
+
     public void testAggNameValidationsWithoutIssues() {
         String prefix = randomAlphaOfLength(10) + "1";
         String prefix2 = randomAlphaOfLength(10) + "2";