diff --git a/src/org/labkey/targetedms/query/TargetedMSForeignKey.java b/src/org/labkey/targetedms/query/TargetedMSForeignKey.java
index 974fa7a9c..1804d7d0e 100644
--- a/src/org/labkey/targetedms/query/TargetedMSForeignKey.java
+++ b/src/org/labkey/targetedms/query/TargetedMSForeignKey.java
@@ -38,8 +38,9 @@ public TargetedMSForeignKey(TargetedMSSchema schema, String tableName, Container
     @Override
     public TableInfo getLookupTableInfo()
     {
-        TableInfo table = _schema.getTable(_tableName);
-        ((TargetedMSTable)table).setNeedsContainerWhereClause(false);
-        return table;
+        // Avoid applying a container filter on lookups. The import process should be only creating FKs to data
+        // in the same container. Thus, we can rely on the outer query doing the proper filtering and avoid
+        // what can be expensive multi-table joins to get to a table that has the Container column we need
+        return _schema.getTable(_tableName, ContainerFilter.EVERYTHING);
     }
 }
diff --git a/src/org/labkey/targetedms/query/TargetedMSTable.java b/src/org/labkey/targetedms/query/TargetedMSTable.java
index f9d0c4e3a..7c6a0c75f 100644
--- a/src/org/labkey/targetedms/query/TargetedMSTable.java
+++ b/src/org/labkey/targetedms/query/TargetedMSTable.java
@@ -89,11 +89,6 @@ protected void applyContainerFilter(ContainerFilter filter)
         // Don't apply the container filter normally, let us apply it in our wrapper around the normally generated SQL
     }
 
-    public void setNeedsContainerWhereClause(boolean needsContainerWhereClause)
-    {
-        _needsContainerWhereClause = needsContainerWhereClause;
-    }
-
     @Override
     @NotNull
     public SQLFragment getFromSQL(String alias)
@@ -102,7 +97,7 @@ public SQLFragment getFromSQL(String alias)
         sql.append(super.getFromSQL("X"));
         sql.append(" ");
 
-        if (_needsContainerWhereClause || _containerTableFilter != null)
+        if (getContainerFilter() != ContainerFilter.EVERYTHING || _containerTableFilter != null)
         {
             sql.append(_joinType != null ? _joinType.getSQL() : "");