diff --git a/jstests/noPassthrough/index_version_autoupgrade.js b/jstests/noPassthrough/index_version_autoupgrade.js
index 6895304217a00..b7dcd5c7f35d6 100644
--- a/jstests/noPassthrough/index_version_autoupgrade.js
+++ b/jstests/noPassthrough/index_version_autoupgrade.js
@@ -42,9 +42,18 @@
         testDB.dropDatabase();
         var coll = testDB.index_version_autoupgrade;
 
-        assert.commandWorked(coll.createIndex({withoutAnyOptions: 1}));
+        // Create a v=1 _id index. This requires setting featureCompatibilityVersion to 3.2.
+        assert.commandWorked(conn.adminCommand({setFeatureCompatibilityVersion: "3.2"}));
+        assert.commandWorked(testDB.createCollection("index_version_autoupgrade"));
+        assert.commandWorked(conn.adminCommand({setFeatureCompatibilityVersion: "3.4"}));
         var allIndexes = coll.getIndexes();
-        var spec = GetIndexHelpers.findByKeyPattern(allIndexes, {withoutAnyOptions: 1});
+        var spec = GetIndexHelpers.findByKeyPattern(allIndexes, {_id: 1});
+        assert.neq(null, spec, "Index with key pattern {_id: 1} not found: " + tojson(allIndexes));
+        assert.eq(1, spec.v, "Expected a v=1 index to be built: " + tojson(spec));
+
+        assert.commandWorked(coll.createIndex({withoutAnyOptions: 1}));
+        allIndexes = coll.getIndexes();
+        spec = GetIndexHelpers.findByKeyPattern(allIndexes, {withoutAnyOptions: 1});
         assert.neq(
             null,
             spec,
@@ -72,6 +81,7 @@
 
         if (doesAutoUpgrade) {
             expectedResults = [
+                {keyPattern: {_id: 1}, version: defaultIndexVersion},
                 {keyPattern: {withoutAnyOptions: 1}, version: defaultIndexVersion},
                 {keyPattern: {withV1: 1}, version: defaultIndexVersion},
                 {keyPattern: {withV2: 1}, version: defaultIndexVersion},
@@ -79,6 +89,7 @@
 
         } else {
             expectedResults = [
+                {keyPattern: {_id: 1}, version: 1},
                 {keyPattern: {withoutAnyOptions: 1}, version: defaultIndexVersion},
                 {keyPattern: {withV1: 1}, version: 1},
                 {keyPattern: {withV2: 1}, version: 2},
@@ -86,7 +97,7 @@
         }
 
         expectedResults.forEach(function(expected) {
-            var allIndexes = coll.getIndexes();
+            var allIndexes = collToVerify.getIndexes();
             var spec = GetIndexHelpers.findByKeyPattern(allIndexes, expected.keyPattern);
             assert.neq(null,
                        spec,
@@ -151,5 +162,19 @@
     }, false);
     MongoRunner.stopMongod(cloneConn);
 
+    // Test that the "clone" command doesn't upgrade existing indexes to the latest version.
+    cloneConn = MongoRunner.runMongod({});
+    assert.neq(null, cloneConn, "mongod was unable to start up");
+    assert.eq("3.4", getFeatureCompatibilityVersion(cloneConn));
+    testIndexVersionAutoUpgrades(function(coll) {
+        var cloneDB = cloneConn.getDB(coll.getDB().getName());
+        assert.commandWorked(cloneDB.runCommand({
+            clone: conn.host,
+            fromDB: coll.getDB().getName(),
+        }));
+        return cloneDB[coll.getName()];
+    }, false);
+    MongoRunner.stopMongod(cloneConn);
+
     MongoRunner.stopMongod(conn);
 })();
diff --git a/jstests/repl/initial_sync_id_index.js b/jstests/repl/initial_sync_id_index.js
new file mode 100644
index 0000000000000..5871f68f3232e
--- /dev/null
+++ b/jstests/repl/initial_sync_id_index.js
@@ -0,0 +1,46 @@
+// Tests that the _id index spec is copied exactly during initial sync.
+(function() {
+    "use strict";
+
+    load("jstests/libs/get_index_helpers.js");
+
+    const rt = new ReplTest();
+    const master = rt.start(true);
+    const masterDB = master.getDB("test");
+
+    // Initially, featureCompatibilityVersion is 3.4, so we will create v=2 indexes.
+    let res = master.adminCommand({getParameter: 1, featureCompatibilityVersion: 1});
+    assert.commandWorked(res);
+    assert.eq(res.featureCompatibilityVersion, "3.4");
+    assert.commandWorked(masterDB.createCollection("collV2"));
+    let spec = GetIndexHelpers.findByName(masterDB.collV2.getIndexes(), "_id_");
+    assert.neq(spec, null);
+    assert.eq(spec.v, 2);
+
+    // Set featureCompatibilityVersion to 3.2, so we create v=1 indexes.
+    assert.commandWorked(master.adminCommand({setFeatureCompatibilityVersion: "3.2"}));
+    res = master.adminCommand({getParameter: 1, featureCompatibilityVersion: 1});
+    assert.commandWorked(res);
+    assert.eq(res.featureCompatibilityVersion, "3.2");
+    assert.commandWorked(masterDB.createCollection("collV1"));
+    spec = GetIndexHelpers.findByName(masterDB.collV1.getIndexes(), "_id_");
+    assert.neq(spec, null);
+    assert.eq(spec.v, 1);
+
+    // Initial sync a slave.
+    const slave = rt.start(false);
+    const slaveDB = slave.getDB("test");
+
+    // Perform a w=2 write to ensure that slave can be read from, and initial sync is complete.
+    assert.writeOK(masterDB.coll.insert({}, {writeConcern: {w: 2}}));
+
+    // Check _id index versions on slave.
+    spec = GetIndexHelpers.findByName(slaveDB.collV2.getIndexes(), "_id_");
+    assert.neq(spec, null);
+    assert.eq(spec.v, 2);
+    spec = GetIndexHelpers.findByName(slaveDB.collV1.getIndexes(), "_id_");
+    assert.neq(spec, null);
+    assert.eq(spec.v, 1);
+
+    rt.stop();
+})();
\ No newline at end of file
diff --git a/src/mongo/db/cloner.cpp b/src/mongo/db/cloner.cpp
index 9d854b8e705f2..c45ed237c44e1 100644
--- a/src/mongo/db/cloner.cpp
+++ b/src/mongo/db/cloner.cpp
@@ -674,10 +674,36 @@ Status Cloner::copyDb(OperationContext* txn,
                 MultiIndexBlock indexer(txn, c);
                 indexer.allowInterruption();
 
-                const auto featureCompatibilityVersion =
-                    serverGlobalParams.featureCompatibility.version.load();
-                auto indexInfoObjs = uassertStatusOK(indexer.init(
-                    c->getIndexCatalog()->getDefaultIdIndexSpec(featureCompatibilityVersion)));
+                BSONObj idIndexSpec;
+                {
+                    Lock::TempRelease tempRelease(txn->lockState());
+                    auto sourceIndexes = _conn->getIndexSpecs(
+                        from_name.ns(), opts.slaveOk ? QueryOption_SlaveOk : 0);
+                    for (auto&& indexSpec : sourceIndexes) {
+                        if ("_id_"_sd == indexSpec["name"].String()) {
+                            idIndexSpec = indexSpec;
+                            break;
+                        }
+                    }
+                }
+
+                uassert(ErrorCodes::NotMaster,
+                        str::stream() << "Not primary while cloning database " << opts.fromDB
+                                      << " (after getting _id index spec for collection "
+                                      << from_name.ns()
+                                      << ")",
+                        !txn->writesAreReplicated() ||
+                            repl::getGlobalReplicationCoordinator()->canAcceptWritesForDatabase(
+                                toDBName));
+
+                uassert(40332,
+                        str::stream() << "_id index spec not found for collection "
+                                      << from_name.ns()
+                                      << " during clone",
+                        !idIndexSpec.isEmpty());
+
+                auto indexInfoObjs = uassertStatusOK(
+                    indexer.init(fixIndexSpec(to_name.db().toString(), idIndexSpec)));
                 invariant(indexInfoObjs.size() == 1);
                 uassertStatusOK(indexer.insertAllDocumentsInCollection(&dups));