diff --git a/cmd/bootstrap/cmd/rootblock.go b/cmd/bootstrap/cmd/rootblock.go
index 505d3239024..7d9f612ee10 100644
--- a/cmd/bootstrap/cmd/rootblock.go
+++ b/cmd/bootstrap/cmd/rootblock.go
@@ -146,7 +146,7 @@ func rootBlock(cmd *cobra.Command, args []string) {
 	}
 
 	log.Info().Msg("collecting partner network and staking keys")
-	partnerNodes, err := common.ReadFullPartnerNodeInfos(log, flagPartnerWeights, flagPartnerNodeInfoDir)
+	rawPartnerNodes, err := common.ReadFullPartnerNodeInfos(log, flagPartnerWeights, flagPartnerNodeInfoDir)
 	if err != nil {
 		log.Fatal().Err(err).Msg("failed to read full partner node infos")
 	}
@@ -160,6 +160,10 @@ func rootBlock(cmd *cobra.Command, args []string) {
 
 	log.Info().Msg("")
 
+	log.Info().Msg("remove internal partner nodes")
+	partnerNodes := common.FilterInternalPartners(rawPartnerNodes, internalNodes)
+	log.Info().Msgf("removed %d internal partner nodes", len(rawPartnerNodes)-len(partnerNodes))
+
 	log.Info().Msg("checking constraints on consensus nodes")
 	checkConstraints(partnerNodes, internalNodes)
 	log.Info().Msg("")
diff --git a/cmd/bootstrap/cmd/rootblock_test.go b/cmd/bootstrap/cmd/rootblock_test.go
index 01222c0c476..8c3080d0b11 100644
--- a/cmd/bootstrap/cmd/rootblock_test.go
+++ b/cmd/bootstrap/cmd/rootblock_test.go
@@ -21,7 +21,10 @@ const rootBlockHappyPathLogs = "collecting partner network and staking keys" +
 	`read \d+ internal private node-info files` +
 	`read internal node configurations` +
 	`read \d+ weights for internal nodes` +
+	`remove internal partner nodes` +
+	`removed 0 internal partner nodes` +
 	`checking constraints on consensus nodes` +
+
 	`assembling network and staking keys` +
 	`wrote file \S+/node-infos.pub.json` +
 	`running DKG for consensus nodes` +
diff --git a/cmd/util/cmd/common/node_info.go b/cmd/util/cmd/common/node_info.go
index 061741d0955..5f9ebb79cd4 100644
--- a/cmd/util/cmd/common/node_info.go
+++ b/cmd/util/cmd/common/node_info.go
@@ -224,3 +224,19 @@ func internalWeightsByAddress(log zerolog.Logger, config string) map[string]uint
 
 	return weights
 }
+
+// Reject any partner nodes that are in the internal node list.
+func FilterInternalPartners(partners []bootstrap.NodeInfo, internal []bootstrap.NodeInfo) []bootstrap.NodeInfo {
+	lookup := make(map[flow.Identifier]struct{})
+	for _, node := range internal {
+		lookup[node.NodeID] = struct{}{}
+	}
+
+	var filtered []bootstrap.NodeInfo
+	for _, node := range partners {
+		if _, ok := lookup[node.NodeID]; !ok {
+			filtered = append(filtered, node)
+		}
+	}
+	return filtered
+}