diff --git a/config/sql/midpoint/3.1.1/h2/h2-3.1.1.sql b/config/sql/midpoint/3.1.1/h2/h2-3.1.1.sql
index c30eddf1289..e26ffd381d8 100644
--- a/config/sql/midpoint/3.1.1/h2/h2-3.1.1.sql
+++ b/config/sql/midpoint/3.1.1/h2/h2-3.1.1.sql
@@ -116,13 +116,13 @@ CREATE TABLE m_assignment_extension (
 );
 
 CREATE TABLE m_assignment_reference (
-  reference_type  INTEGER      NOT NULL,
   owner_id        SMALLINT     NOT NULL,
   owner_owner_oid VARCHAR(36)  NOT NULL,
+  reference_type  INTEGER      NOT NULL,
   relation        VARCHAR(157) NOT NULL,
   targetOid       VARCHAR(36)  NOT NULL,
   containerType   INTEGER,
-  PRIMARY KEY (owner_id, owner_owner_oid, relation, targetOid)
+  PRIMARY KEY (owner_id, owner_owner_oid, reference_type, relation, targetOid)
 );
 
 CREATE TABLE m_audit_delta (
@@ -369,12 +369,12 @@ CREATE TABLE m_org_org_type (
 );
 
 CREATE TABLE m_reference (
-  reference_type INTEGER      NOT NULL,
   owner_oid      VARCHAR(36)  NOT NULL,
+  reference_type INTEGER      NOT NULL,
   relation       VARCHAR(157) NOT NULL,
   targetOid      VARCHAR(36)  NOT NULL,
   containerType  INTEGER,
-  PRIMARY KEY (owner_oid, relation, targetOid)
+  PRIMARY KEY (owner_oid, reference_type, relation, targetOid)
 );
 
 CREATE TABLE m_report (
@@ -758,7 +758,7 @@ FOREIGN KEY (oid)
 REFERENCES m_object;
 
 ALTER TABLE m_lookup_table_row
-ADD CONSTRAINT fk_lookup_table
+ADD CONSTRAINT fk_lookup_table_owner
 FOREIGN KEY (owner_oid)
 REFERENCES m_lookup_table;
 
diff --git a/config/sql/midpoint/3.1.1/h2/h2-upgrade-3.1-3.1.1.sql b/config/sql/midpoint/3.1.1/h2/h2-upgrade-3.1-3.1.1.sql
index 70d088fb182..7607dee7130 100644
--- a/config/sql/midpoint/3.1.1/h2/h2-upgrade-3.1-3.1.1.sql
+++ b/config/sql/midpoint/3.1.1/h2/h2-upgrade-3.1-3.1.1.sql
@@ -24,6 +24,18 @@ FOREIGN KEY (oid)
 REFERENCES m_object;
 
 ALTER TABLE m_lookup_table_row
-ADD CONSTRAINT fk_lookup_table
+ADD CONSTRAINT fk_lookup_table_owner
 FOREIGN KEY (owner_oid)
-REFERENCES m_lookup_table;
\ No newline at end of file
+REFERENCES m_lookup_table;
+
+ALTER TABLE m_assignment_reference
+DROP PRIMARY KEY;
+
+ALTER TABLE m_assignment_reference
+ADD PRIMARY KEY (owner_id, owner_owner_oid, reference_type, relation, targetOid);
+
+ALTER TABLE m_reference
+DROP PRIMARY KEY;
+
+ALTER TABLE m_reference
+ADD PRIMARY KEY (owner_oid, reference_type, relation, targetOid);
\ No newline at end of file
diff --git a/config/sql/midpoint/3.1.1/mysql/mysql-3.1.1.sql b/config/sql/midpoint/3.1.1/mysql/mysql-3.1.1.sql
index 44511d718bf..2c0597ebdac 100644
--- a/config/sql/midpoint/3.1.1/mysql/mysql-3.1.1.sql
+++ b/config/sql/midpoint/3.1.1/mysql/mysql-3.1.1.sql
@@ -153,13 +153,13 @@ CREATE TABLE m_assignment_extension (
   ENGINE = InnoDB;
 
 CREATE TABLE m_assignment_reference (
-  reference_type  INTEGER      NOT NULL,
   owner_id        SMALLINT     NOT NULL,
   owner_owner_oid VARCHAR(36)  NOT NULL,
+  reference_type  INTEGER      NOT NULL,
   relation        VARCHAR(157) NOT NULL,
   targetOid       VARCHAR(36)  NOT NULL,
   containerType   INTEGER,
-  PRIMARY KEY (owner_id, owner_owner_oid, relation, targetOid)
+  PRIMARY KEY (owner_id, owner_owner_oid, reference_type, relation, targetOid)
 )
   DEFAULT CHARACTER SET utf8
   COLLATE utf8_bin
@@ -472,12 +472,12 @@ CREATE TABLE m_org_org_type (
   ENGINE = InnoDB;
 
 CREATE TABLE m_reference (
-  reference_type INTEGER      NOT NULL,
   owner_oid      VARCHAR(36)  NOT NULL,
+  reference_type INTEGER      NOT NULL,
   relation       VARCHAR(157) NOT NULL,
   targetOid      VARCHAR(36)  NOT NULL,
   containerType  INTEGER,
-  PRIMARY KEY (owner_oid, relation, targetOid)
+  PRIMARY KEY (owner_oid, reference_type, relation, targetOid)
 )
   DEFAULT CHARACTER SET utf8
   COLLATE utf8_bin
@@ -914,7 +914,7 @@ FOREIGN KEY (oid)
 REFERENCES m_object (oid);
 
 ALTER TABLE m_lookup_table_row
-ADD CONSTRAINT fk_lookup_table
+ADD CONSTRAINT fk_lookup_table_owner
 FOREIGN KEY (owner_oid)
 REFERENCES m_lookup_table (oid);
 
diff --git a/config/sql/midpoint/3.1.1/mysql/mysql-upgrade-3.1-3.1.1.sql b/config/sql/midpoint/3.1.1/mysql/mysql-upgrade-3.1-3.1.1.sql
index ee9e9c7ab99..ba45e6e3130 100644
--- a/config/sql/midpoint/3.1.1/mysql/mysql-upgrade-3.1-3.1.1.sql
+++ b/config/sql/midpoint/3.1.1/mysql/mysql-upgrade-3.1-3.1.1.sql
@@ -30,6 +30,14 @@ FOREIGN KEY (oid)
 REFERENCES m_object (oid);
 
 ALTER TABLE m_lookup_table_row
-ADD CONSTRAINT fk_lookup_table
+ADD CONSTRAINT fk_lookup_table_owner
 FOREIGN KEY (owner_oid)
-REFERENCES m_lookup_table (oid);
\ No newline at end of file
+REFERENCES m_lookup_table (oid);
+
+ALTER TABLE m_assignment_reference
+DROP PRIMARY KEY,
+ADD PRIMARY KEY (owner_id, owner_owner_oid, reference_type, relation, targetOid);
+
+ALTER TABLE m_reference
+DROP PRIMARY KEY,
+ADD PRIMARY KEY (owner_oid, reference_type, relation, targetOid);
\ No newline at end of file
diff --git a/config/sql/midpoint/3.1.1/postgresql/postgresql-3.1.1.sql b/config/sql/midpoint/3.1.1/postgresql/postgresql-3.1.1.sql
index 3ee6bb7cc63..e8906702e27 100644
--- a/config/sql/midpoint/3.1.1/postgresql/postgresql-3.1.1.sql
+++ b/config/sql/midpoint/3.1.1/postgresql/postgresql-3.1.1.sql
@@ -116,13 +116,13 @@ CREATE TABLE m_assignment_extension (
 );
 
 CREATE TABLE m_assignment_reference (
-  reference_type  INT4         NOT NULL,
   owner_id        INT2         NOT NULL,
   owner_owner_oid VARCHAR(36)  NOT NULL,
+  reference_type  INT4         NOT NULL,
   relation        VARCHAR(157) NOT NULL,
   targetOid       VARCHAR(36)  NOT NULL,
   containerType   INT4,
-  PRIMARY KEY (owner_id, owner_owner_oid, relation, targetOid)
+  PRIMARY KEY (owner_id, owner_owner_oid, reference_type, relation, targetOid)
 );
 
 CREATE TABLE m_audit_delta (
@@ -369,12 +369,12 @@ CREATE TABLE m_org_org_type (
 );
 
 CREATE TABLE m_reference (
-  reference_type INT4         NOT NULL,
   owner_oid      VARCHAR(36)  NOT NULL,
+  reference_type INT4         NOT NULL,
   relation       VARCHAR(157) NOT NULL,
   targetOid      VARCHAR(36)  NOT NULL,
   containerType  INT4,
-  PRIMARY KEY (owner_oid, relation, targetOid)
+  PRIMARY KEY (owner_oid, reference_type, relation, targetOid)
 );
 
 CREATE TABLE m_report (
@@ -758,7 +758,7 @@ FOREIGN KEY (oid)
 REFERENCES m_object;
 
 ALTER TABLE m_lookup_table_row
-ADD CONSTRAINT fk_lookup_table
+ADD CONSTRAINT fk_lookup_table_owner
 FOREIGN KEY (owner_oid)
 REFERENCES m_lookup_table;
 
diff --git a/config/sql/midpoint/3.1.1/postgresql/postgresql-upgrade-3.1-3.1.1.sql b/config/sql/midpoint/3.1.1/postgresql/postgresql-upgrade-3.1-3.1.1.sql
index 93f161c3795..494285574db 100644
--- a/config/sql/midpoint/3.1.1/postgresql/postgresql-upgrade-3.1-3.1.1.sql
+++ b/config/sql/midpoint/3.1.1/postgresql/postgresql-upgrade-3.1-3.1.1.sql
@@ -24,6 +24,14 @@ FOREIGN KEY (oid)
 REFERENCES m_object;
 
 ALTER TABLE m_lookup_table_row
-ADD CONSTRAINT fk_lookup_table
+ADD CONSTRAINT fk_lookup_table_owner
 FOREIGN KEY (owner_oid)
 REFERENCES m_lookup_table;
+
+ALTER TABLE m_assignment_reference
+DROP CONSTRAINT m_assignment_reference_pkey,
+ADD CONSTRAINT m_assignment_reference_pkey PRIMARY KEY (owner_id, owner_owner_oid, reference_type, relation, targetOid);
+
+ALTER TABLE m_reference
+DROP CONSTRAINT m_reference_pkey,
+ADD CONSTRAINT m_reference_pkey PRIMARY KEY (owner_oid, reference_type, relation, targetOid);