diff --git a/.deadcode-out b/.deadcode-out
index 61c5bcb055..0e3a97ffa8 100644
--- a/.deadcode-out
+++ b/.deadcode-out
@@ -27,6 +27,7 @@ forgejo.org/models/db
 	TruncateBeans
 	InTransaction
 	DumpTables
+	GetTableNames
 
 forgejo.org/models/dbfs
 	file.renameTo
diff --git a/models/asymkey/main_test.go b/models/asymkey/main_test.go
index 316e8f1d54..aa13a93f0a 100644
--- a/models/asymkey/main_test.go
+++ b/models/asymkey/main_test.go
@@ -15,8 +15,6 @@ func TestMain(m *testing.M) {
 			"gpg_key.yml",
 			"public_key.yml",
 			"TestParseCommitWithSSHSignature/public_key.yml",
-			"deploy_key.yml",
-			"gpg_key_import.yml",
 			"user.yml",
 			"email_address.yml",
 		},
diff --git a/models/db/engine.go b/models/db/engine.go
index 05a119b08d..76025f7d67 100755
--- a/models/db/engine.go
+++ b/models/db/engine.go
@@ -15,6 +15,7 @@ import (
 	"strings"
 	"time"
 
+	"forgejo.org/modules/container"
 	"forgejo.org/modules/log"
 	"forgejo.org/modules/setting"
 
@@ -438,3 +439,12 @@ func GetMasterEngine(x Engine) (*xorm.Engine, error) {
 
 	return engine, nil
 }
+
+// GetTableNames returns the table name of all registered models.
+func GetTableNames() container.Set[string] {
+	names := make(container.Set[string])
+	for _, table := range tables {
+		names.Add(x.TableName(table))
+	}
+	return names
+}
diff --git a/models/db/table_names_test.go b/models/db/table_names_test.go
new file mode 100644
index 0000000000..176ce9905d
--- /dev/null
+++ b/models/db/table_names_test.go
@@ -0,0 +1,40 @@
+// Copyright 2025 The Forgejo Authors. All rights reserved.
+// SPDX-License-Identifier: GPL-3.0-or-later
+
+package db
+
+import (
+	"slices"
+	"testing"
+
+	"forgejo.org/modules/test"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestGetTableNames(t *testing.T) {
+	t.Run("Simple", func(t *testing.T) {
+		defer test.MockVariableValue(&tables, []any{new(GPGKey)})()
+
+		assert.Equal(t, []string{"gpg_key"}, GetTableNames().Values())
+	})
+
+	t.Run("Multiple tables", func(t *testing.T) {
+		defer test.MockVariableValue(&tables, []any{new(GPGKey), new(User), new(BlockedUser)})()
+
+		tableNames := GetTableNames().Values()
+		slices.Sort(tableNames)
+
+		assert.Equal(t, []string{"forgejo_blocked_user", "gpg_key", "user"}, tableNames)
+	})
+}
+
+type GPGKey struct{}
+
+type User struct{}
+
+type BlockedUser struct{}
+
+func (*BlockedUser) TableName() string {
+	return "forgejo_blocked_user"
+}
diff --git a/models/fixtures/action_variable.yml b/models/fixtures/action_variable.yml
deleted file mode 100644
index ca780a73aa..0000000000
--- a/models/fixtures/action_variable.yml
+++ /dev/null
@@ -1 +0,0 @@
-[] # empty
diff --git a/models/fixtures/deploy_key.yml b/models/fixtures/deploy_key.yml
deleted file mode 100644
index ca780a73aa..0000000000
--- a/models/fixtures/deploy_key.yml
+++ /dev/null
@@ -1 +0,0 @@
-[] # empty
diff --git a/models/fixtures/external_login_user.yml b/models/fixtures/external_login_user.yml
deleted file mode 100644
index ca780a73aa..0000000000
--- a/models/fixtures/external_login_user.yml
+++ /dev/null
@@ -1 +0,0 @@
-[] # empty
diff --git a/models/fixtures/federated_user.yml b/models/fixtures/federated_user.yml
deleted file mode 100644
index ca780a73aa..0000000000
--- a/models/fixtures/federated_user.yml
+++ /dev/null
@@ -1 +0,0 @@
-[] # empty
diff --git a/models/fixtures/federation_host.yml b/models/fixtures/federation_host.yml
deleted file mode 100644
index ca780a73aa..0000000000
--- a/models/fixtures/federation_host.yml
+++ /dev/null
@@ -1 +0,0 @@
-[] # empty
diff --git a/models/fixtures/gpg_key_import.yml b/models/fixtures/gpg_key_import.yml
deleted file mode 100644
index ca780a73aa..0000000000
--- a/models/fixtures/gpg_key_import.yml
+++ /dev/null
@@ -1 +0,0 @@
-[] # empty
diff --git a/models/fixtures/login_source.yml b/models/fixtures/login_source.yml
deleted file mode 100644
index ca780a73aa..0000000000
--- a/models/fixtures/login_source.yml
+++ /dev/null
@@ -1 +0,0 @@
-[] # empty
diff --git a/models/fixtures/protected_branch.yml b/models/fixtures/protected_branch.yml
deleted file mode 100644
index ca780a73aa..0000000000
--- a/models/fixtures/protected_branch.yml
+++ /dev/null
@@ -1 +0,0 @@
-[] # empty
diff --git a/models/fixtures/pull_auto_merge.yml b/models/fixtures/pull_auto_merge.yml
deleted file mode 100644
index ca780a73aa..0000000000
--- a/models/fixtures/pull_auto_merge.yml
+++ /dev/null
@@ -1 +0,0 @@
-[] # empty
diff --git a/models/fixtures/push_mirror.yml b/models/fixtures/push_mirror.yml
deleted file mode 100644
index ca780a73aa..0000000000
--- a/models/fixtures/push_mirror.yml
+++ /dev/null
@@ -1 +0,0 @@
-[] # empty
diff --git a/models/fixtures/repo_archiver.yml b/models/fixtures/repo_archiver.yml
deleted file mode 100644
index ca780a73aa..0000000000
--- a/models/fixtures/repo_archiver.yml
+++ /dev/null
@@ -1 +0,0 @@
-[] # empty
diff --git a/models/fixtures/repo_indexer_status.yml b/models/fixtures/repo_indexer_status.yml
deleted file mode 100644
index ca780a73aa..0000000000
--- a/models/fixtures/repo_indexer_status.yml
+++ /dev/null
@@ -1 +0,0 @@
-[] # empty
diff --git a/models/fixtures/secret.yml b/models/fixtures/secret.yml
deleted file mode 100644
index ca780a73aa..0000000000
--- a/models/fixtures/secret.yml
+++ /dev/null
@@ -1 +0,0 @@
-[] # empty
diff --git a/models/migrations/test/tests.go b/models/migrations/test/tests.go
index c1f0caf19b..6be3b3c2fc 100644
--- a/models/migrations/test/tests.go
+++ b/models/migrations/test/tests.go
@@ -95,7 +95,8 @@ func PrepareTestEnv(t *testing.T, skip int, syncModels ...any) (*xorm.Engine, fu
 		t.Logf("initializing fixtures from: %s", fixturesDir)
 		if err := unittest.InitFixtures(
 			unittest.FixturesOptions{
-				Dir: fixturesDir,
+				Dir:                     fixturesDir,
+				SkipCleanRegistedModels: true,
 			}, x); err != nil {
 			t.Errorf("error whilst initializing fixtures from %s: %v", fixturesDir, err)
 			return x, deferFn
diff --git a/models/unittest/fixture_loader.go b/models/unittest/fixture_loader.go
index 67ef1b28df..dda5c48d35 100644
--- a/models/unittest/fixture_loader.go
+++ b/models/unittest/fixture_loader.go
@@ -12,6 +12,8 @@ import (
 	"path/filepath"
 	"strings"
 
+	"forgejo.org/modules/container"
+
 	"gopkg.in/yaml.v3"
 )
 
@@ -32,13 +34,15 @@ type loader struct {
 	fixtureFiles []*fixtureFile
 }
 
-func newFixtureLoader(db *sql.DB, dialect string, fixturePaths []string) (*loader, error) {
+func newFixtureLoader(db *sql.DB, dialect string, fixturePaths []string, allTableNames container.Set[string]) (*loader, error) {
 	l := &loader{
 		db:           db,
 		dialect:      dialect,
 		fixtureFiles: []*fixtureFile{},
 	}
 
+	tablesWithoutFixture := allTableNames
+
 	// Load fixtures
 	for _, fixturePath := range fixturePaths {
 		stat, err := os.Stat(fixturePath)
@@ -60,6 +64,7 @@ func newFixtureLoader(db *sql.DB, dialect string, fixturePaths []string) (*loade
 						return nil, err
 					}
 					l.fixtureFiles = append(l.fixtureFiles, fixtureFile)
+					tablesWithoutFixture.Remove(fixtureFile.name)
 				}
 			}
 		} else {
@@ -71,6 +76,14 @@ func newFixtureLoader(db *sql.DB, dialect string, fixturePaths []string) (*loade
 		}
 	}
 
+	// Even though these tables have no fixtures, they can still be used and ensure
+	// they are cleaned.
+	for table := range tablesWithoutFixture.Seq() {
+		l.fixtureFiles = append(l.fixtureFiles, &fixtureFile{
+			name: table,
+		})
+	}
+
 	return l, nil
 }
 
@@ -178,13 +191,13 @@ func (l *loader) Load() error {
 	}()
 
 	// Clean the table and re-insert the fixtures.
-	tableDeleted := map[string]struct{}{}
+	tableDeleted := make(container.Set[string])
 	for _, fixture := range l.fixtureFiles {
-		if _, ok := tableDeleted[fixture.name]; !ok {
+		if !tableDeleted.Contains(fixture.name) {
 			if _, err := tx.Exec(fmt.Sprintf("DELETE FROM %s", l.quoteKeyword(fixture.name))); err != nil {
 				return fmt.Errorf("cannot delete table %s: %w", fixture.name, err)
 			}
-			tableDeleted[fixture.name] = struct{}{}
+			tableDeleted.Add(fixture.name)
 		}
 
 		for _, insertSQL := range fixture.insertSQLs {
diff --git a/models/unittest/fixtures.go b/models/unittest/fixtures.go
index 6dc5c8412d..829cc16466 100644
--- a/models/unittest/fixtures.go
+++ b/models/unittest/fixtures.go
@@ -7,10 +7,12 @@ package unittest
 import (
 	"fmt"
 	"path/filepath"
+	"sync"
 	"time"
 
 	"forgejo.org/models/db"
 	"forgejo.org/modules/auth/password/hash"
+	"forgejo.org/modules/container"
 	"forgejo.org/modules/setting"
 
 	"xorm.io/xorm"
@@ -44,6 +46,8 @@ func OverrideFixtures(dir string) func() {
 	}
 }
 
+var allTableNames = sync.OnceValue(db.GetTableNames)
+
 // InitFixtures initialize test fixtures for a test database
 func InitFixtures(opts FixturesOptions, engine ...*xorm.Engine) (err error) {
 	e, err := GetXORMEngine(engine...)
@@ -75,7 +79,12 @@ func InitFixtures(opts FixturesOptions, engine ...*xorm.Engine) (err error) {
 		panic("Unsupported RDBMS for test")
 	}
 
-	fixturesLoader, err = newFixtureLoader(e.DB().DB, dialect, fixturePaths)
+	var allTables container.Set[string]
+	if !opts.SkipCleanRegistedModels {
+		allTables = allTableNames().Clone()
+	}
+
+	fixturesLoader, err = newFixtureLoader(e.DB().DB, dialect, fixturePaths, allTables)
 	if err != nil {
 		return err
 	}
diff --git a/models/unittest/testdb.go b/models/unittest/testdb.go
index d34c9e9a0a..29ec82c55f 100644
--- a/models/unittest/testdb.go
+++ b/models/unittest/testdb.go
@@ -217,6 +217,10 @@ type FixturesOptions struct {
 	Files []string
 	Dirs  []string
 	Base  string
+	// By default all registered models are cleaned, even if they do not have
+	// fixture. Enabling this will skip that and only models with fixtures are
+	// considered.
+	SkipCleanRegistedModels bool
 }
 
 // CreateTestEngine creates a memory database and loads the fixture data from fixturesDir
diff --git a/modules/container/set.go b/modules/container/set.go
index 70f837bc66..d3719dc552 100644
--- a/modules/container/set.go
+++ b/modules/container/set.go
@@ -74,3 +74,8 @@ func (s Set[T]) Values() []T {
 func (s Set[T]) Seq() iter.Seq[T] {
 	return maps.Keys(s)
 }
+
+// Clone returns a identical shallow copy of this set.
+func (s Set[T]) Clone() Set[T] {
+	return maps.Clone(s)
+}
diff --git a/modules/container/set_test.go b/modules/container/set_test.go
index af5e9126ab..44e4847f6b 100644
--- a/modules/container/set_test.go
+++ b/modules/container/set_test.go
@@ -47,4 +47,11 @@ func TestSet(t *testing.T) {
 	assert.False(t, s.IsSubset([]string{"key1"}))
 
 	assert.True(t, s.IsSubset([]string{}))
+
+	t.Run("Clone", func(t *testing.T) {
+		clonedSet := s.Clone()
+		clonedSet.Remove("key6")
+		assert.False(t, clonedSet.Contains("key6"))
+		assert.True(t, s.Contains("key6"))
+	})
 }