diff --git a/application/clicommands/CheckCommand.php b/application/clicommands/CheckCommand.php
index 053ef9a4..75e5d2da 100644
--- a/application/clicommands/CheckCommand.php
+++ b/application/clicommands/CheckCommand.php
@@ -92,7 +92,16 @@ public function hostAction()
         $validFrom
             ->columns([new Expression('MAX(GREATEST(%s, %s))', ['valid_from', 'issuer_certificate.valid_from'])])
             ->getSelectBase()
+            // Reset the where clause generated within the createSubQuery() method.
             ->resetWhere()
+            // If the issuer of the current cert is an intermediate one, then we should take its valid_to
+            // timestamp into account unconditionally, ...
+            ->where(new Expression("sub_certificate_issuer_certificate.self_signed = 'n'"))
+            // ... otherwise, since we don't enforce the subject_hash of the certificates to be unambiguous,
+            // we might have more than one self-singed/trusted CA with the same CN and hash but different validity
+            // timestamps, and in such situations we need to make sure that we are joining to the correct CA that
+            // is part of the chain, and not some random one that seems to have the same subject_hash.
+            ->orWhere(new Expression('sub_certificate_link.certificate_id = sub_certificate_issuer_certificate.id'))
             ->where(new Expression('sub_certificate_link.certificate_chain_id = target_chain.id'));
 
         // Sub query for `valid_to` column
@@ -102,6 +111,14 @@ public function hostAction()
             ->getSelectBase()
             // Reset the where clause generated within the createSubQuery() method.
             ->resetWhere()
+            // If the issuer of the current cert is an intermediate one, then we should take its valid_to
+            // timestamp into account unconditionally, ...
+            ->where(new Expression("sub_certificate_issuer_certificate.self_signed = 'n'"))
+            // ... otherwise, since we don't enforce the subject_hash of the certificates to be unambiguous,
+            // we might have more than one self-singed/trusted CA with the same CN and hash but different validity
+            // timestamps, and in such situations we need to make sure that we are joining to the correct CA that
+            // is part of the chain, and not some random one that seems to have the same subject_hash.
+            ->orWhere(new Expression('sub_certificate_link.certificate_id = sub_certificate_issuer_certificate.id'))
             ->where(new Expression('sub_certificate_link.certificate_chain_id = target_chain.id'));
 
         list($validFromSelect, $_) = $validFrom->dump();
diff --git a/library/X509/Job.php b/library/X509/Job.php
index e800a8ee..bebf57bb 100644
--- a/library/X509/Job.php
+++ b/library/X509/Job.php
@@ -721,6 +721,8 @@ protected function processChain($target, $chain)
                     ->columns(['id'])
                     ->filter(Filter::equal('subject_hash', $lastCertInfo[1]))
                     ->filter(Filter::equal('self_signed', true))
+                    // If there are multiple CAs with the same subject hash, pick the newly imported one.
+                    ->orderBy('ctime', SORT_DESC)
                     ->first();
 
                 if ($rootCa && $rootCa->id !== (int) $lastCertInfo[0]) {