diff --git a/src/NHibernate.Test/Async/NHSpecificTest/GH2549/Fixture.cs b/src/NHibernate.Test/Async/NHSpecificTest/GH2549/Fixture.cs
index 82227867203..63ef36ffe09 100644
--- a/src/NHibernate.Test/Async/NHSpecificTest/GH2549/Fixture.cs
+++ b/src/NHibernate.Test/Async/NHSpecificTest/GH2549/Fixture.cs
@@ -15,6 +15,7 @@
 namespace NHibernate.Test.NHSpecificTest.GH2549
 {
 	using System.Threading.Tasks;
+	// Test GH3046 too, when useManyToOne is <c>true</c>.
 	[TestFixture]
 	public class FixtureAsync : BugTestCase
 	{
@@ -41,8 +42,8 @@ protected override void OnTearDown()
 			}
 		}
 
-		[Test]
-		public async Task EntityJoinFilterLinqAsync()
+		[Theory]
+		public async Task EntityJoinFilterLinqAsync(bool useManyToOne)
 		{
 			using (var s = OpenSession())
 			{
@@ -50,7 +51,7 @@ public async Task EntityJoinFilterLinqAsync()
 							join c in s.Query<Customer>() on p.Name equals c.Name
 							select p).ToListAsync());
 
-				s.EnableFilter("DeletedCustomer").SetParameter("deleted", false);
+				s.EnableFilter(useManyToOne ? "DeletedCustomer" : "DeletedCustomerNoManyToOne").SetParameter("deleted", false);
 
 				var filteredList = await ((from p in s.Query<Person>()
 									join c in s.Query<Customer>() on p.Name equals c.Name
@@ -61,8 +62,8 @@ join c in s.Query<Customer>() on p.Name equals c.Name
 			}
 		}
 
-		[Test]
-		public async Task EntityJoinFilterQueryOverAsync()
+		[Theory]
+		public async Task EntityJoinFilterQueryOverAsync(bool useManyToOne)
 		{
 			using (var s = OpenSession())
 			{
@@ -70,7 +71,7 @@ public async Task EntityJoinFilterQueryOverAsync()
 				Person p = null;
 				var list = await (s.QueryOver(() => p).JoinEntityAlias(() => c, () => c.Name == p.Name).ListAsync());
 
-				s.EnableFilter("DeletedCustomer").SetParameter("deleted", false);
+				s.EnableFilter(useManyToOne ? "DeletedCustomer" : "DeletedCustomerNoManyToOne").SetParameter("deleted", false);
 
 				var filteredList = await (s.QueryOver(() => p).JoinEntityAlias(() => c, () => c.Name == p.Name).ListAsync());
 
diff --git a/src/NHibernate.Test/NHSpecificTest/GH2549/Fixture.cs b/src/NHibernate.Test/NHSpecificTest/GH2549/Fixture.cs
index a01c1ec2572..8912bec9a25 100644
--- a/src/NHibernate.Test/NHSpecificTest/GH2549/Fixture.cs
+++ b/src/NHibernate.Test/NHSpecificTest/GH2549/Fixture.cs
@@ -3,6 +3,7 @@
 
 namespace NHibernate.Test.NHSpecificTest.GH2549
 {
+	// Test GH3046 too, when useManyToOne is <c>true</c>.
 	[TestFixture]
 	public class Fixture : BugTestCase
 	{
@@ -29,8 +30,8 @@ protected override void OnTearDown()
 			}
 		}
 
-		[Test]
-		public void EntityJoinFilterLinq()
+		[Theory]
+		public void EntityJoinFilterLinq(bool useManyToOne)
 		{
 			using (var s = OpenSession())
 			{
@@ -38,7 +39,7 @@ public void EntityJoinFilterLinq()
 							join c in s.Query<Customer>() on p.Name equals c.Name
 							select p).ToList();
 
-				s.EnableFilter("DeletedCustomer").SetParameter("deleted", false);
+				s.EnableFilter(useManyToOne ? "DeletedCustomer" : "DeletedCustomerNoManyToOne").SetParameter("deleted", false);
 
 				var filteredList = (from p in s.Query<Person>()
 									join c in s.Query<Customer>() on p.Name equals c.Name
@@ -49,8 +50,8 @@ join c in s.Query<Customer>() on p.Name equals c.Name
 			}
 		}
 
-		[Test]
-		public void EntityJoinFilterQueryOver()
+		[Theory]
+		public void EntityJoinFilterQueryOver(bool useManyToOne)
 		{
 			using (var s = OpenSession())
 			{
@@ -58,7 +59,7 @@ public void EntityJoinFilterQueryOver()
 				Person p = null;
 				var list = s.QueryOver(() => p).JoinEntityAlias(() => c, () => c.Name == p.Name).List();
 
-				s.EnableFilter("DeletedCustomer").SetParameter("deleted", false);
+				s.EnableFilter(useManyToOne ? "DeletedCustomer" : "DeletedCustomerNoManyToOne").SetParameter("deleted", false);
 
 				var filteredList = s.QueryOver(() => p).JoinEntityAlias(() => c, () => c.Name == p.Name).List();
 
diff --git a/src/NHibernate.Test/NHSpecificTest/GH2549/Mappings.hbm.xml b/src/NHibernate.Test/NHSpecificTest/GH2549/Mappings.hbm.xml
index 65b540b9202..de096391e88 100644
--- a/src/NHibernate.Test/NHSpecificTest/GH2549/Mappings.hbm.xml
+++ b/src/NHibernate.Test/NHSpecificTest/GH2549/Mappings.hbm.xml
@@ -10,6 +10,7 @@
       <property name="Deleted" type="Boolean" not-null="true" />
 
       <filter name="DeletedCustomer" condition="Deleted = :deleted" />
+      <filter name="DeletedCustomerNoManyToOne" condition="Deleted = :deleted" />
     </class>
 
     <class name="Person">
@@ -23,4 +24,8 @@
         <filter-param name="deleted" type="Boolean"/>
     </filter-def>
 
+    <filter-def name="DeletedCustomerNoManyToOne" use-many-to-one="false">
+        <filter-param name="deleted" type="Boolean"/>
+    </filter-def>
+
 </hibernate-mapping>
diff --git a/src/NHibernate/Engine/JoinSequence.cs b/src/NHibernate/Engine/JoinSequence.cs
index e706d97886e..0682cc10df5 100644
--- a/src/NHibernate/Engine/JoinSequence.cs
+++ b/src/NHibernate/Engine/JoinSequence.cs
@@ -175,7 +175,7 @@ internal virtual JoinFragment ToJoinFragment(
 			{
 				Join join = joins[i];
 				string on = join.AssociationType.GetOnCondition(join.Alias, factory, enabledFilters);
-				SqlString condition = new SqlString();
+				SqlString condition;
 				if (last != null &&
 						IsManyToManyRoot(last) &&
 						((IQueryableCollection)last).ElementType == join.AssociationType)
@@ -195,10 +195,17 @@ internal virtual JoinFragment ToJoinFragment(
 				{
 					// NH Different behavior : NH1179 and NH1293
 					// Apply filters for entity joins and Many-To-One association
-					var enabledForManyToOne = FilterHelper.GetEnabledForManyToOne(enabledFilters);
-					condition = new SqlString(string.IsNullOrEmpty(on) && (ForceFilter || enabledForManyToOne.Count > 0)
-					            	? join.Joinable.FilterFragment(join.Alias, enabledForManyToOne)
-					            	: on);
+					if (string.IsNullOrEmpty(on))
+					{
+						var enabledFiltersForJoin = ForceFilter ? enabledFilters : FilterHelper.GetEnabledForManyToOne(enabledFilters);
+						condition = new SqlString(ForceFilter || enabledFiltersForJoin.Count > 0
+										? join.Joinable.FilterFragment(join.Alias, enabledFiltersForJoin)
+										: on);
+					}
+					else
+					{
+						condition = new SqlString(on);
+					}
 				}
 
 				if (withClauseFragment != null)
diff --git a/src/NHibernate/Loader/JoinWalker.cs b/src/NHibernate/Loader/JoinWalker.cs
index 1f1ed70fc56..ff02c24306d 100644
--- a/src/NHibernate/Loader/JoinWalker.cs
+++ b/src/NHibernate/Loader/JoinWalker.cs
@@ -853,9 +853,10 @@ protected JoinFragment MergeOuterJoins(IList<OuterJoinableAssociation> associati
 					oj.AddJoins(outerjoin);
 					// NH Different behavior : NH1179 and NH1293
 					// Apply filters for entity joins and Many-To-One associations
-					if (oj.ForceFilter || enabledFiltersForManyToOne.Count > 0)
+					var enabledFiltersForJoin = oj.ForceFilter ? enabledFilters : enabledFiltersForManyToOne;
+					if (oj.ForceFilter || enabledFiltersForJoin.Count > 0)
 					{
-						string manyToOneFilterFragment = oj.Joinable.FilterFragment(oj.RHSAlias, enabledFiltersForManyToOne);
+						string manyToOneFilterFragment = oj.Joinable.FilterFragment(oj.RHSAlias, enabledFiltersForJoin);
 						bool joinClauseDoesNotContainsFilterAlready =
 							outerjoin.ToFromFragmentString.IndexOfCaseInsensitive(manyToOneFilterFragment) == -1;
 						if (joinClauseDoesNotContainsFilterAlready)