diff --git a/packages/tables/src/Filters/SelectFilter.php b/packages/tables/src/Filters/SelectFilter.php
index dda0cca0082..383b38ab1a6 100644
--- a/packages/tables/src/Filters/SelectFilter.php
+++ b/packages/tables/src/Filters/SelectFilter.php
@@ -41,6 +41,8 @@ class SelectFilter extends BaseFilter
 
     protected ?Closure $getOptionLabelFromRecordUsing = null;
 
+    protected const EMPTY_RELATIONSHIP_OPTION_KEY = '__empty';
+
     protected function setUp(): void
     {
         parent::setUp();
@@ -64,7 +66,7 @@ protected function setUp(): void
 
                     if (
                         $filter->hasEmptyRelationshipOption() &&
-                        in_array('__empty', $state['values'])
+                        in_array(static::EMPTY_RELATIONSHIP_OPTION_KEY, $state['values'])
                     ) {
                         $labels[] = $filter->getEmptyRelationshipOptionLabel();
                     }
@@ -78,7 +80,7 @@ protected function setUp(): void
                             )
                             ->when(
                                 $filter->getRelationshipKey(),
-                                fn (Builder $query, string $relationshipKey) => $query->whereIn($relationshipKey, $state['values']),
+                                fn (Builder $query, string $relationshipKey) => $query->whereIn($relationshipKey, $filter->getRelationshipQueryValues($state['values'])),
                                 fn (Builder $query) => $query->whereKey($state['values'])
                             )
                             ->pluck($relationshipQuery->qualifyColumn($filter->getRelationshipTitleAttribute()))
@@ -113,7 +115,7 @@ protected function setUp(): void
             if ($filter->queriesRelationships()) {
                 if (
                     $filter->hasEmptyRelationshipOption() &&
-                    ($state['value'] === '__empty')
+                    ($state['value'] === static::EMPTY_RELATIONSHIP_OPTION_KEY)
                 ) {
                     $label = $filter->getEmptyRelationshipOptionLabel();
                 } else {
@@ -192,33 +194,49 @@ public function apply(Builder $query, array $data = []): Builder
             );
         }
 
-        $applyRelationshipScope = fn (Builder $query) => $query->whereHas(
-            $this->getRelationshipName(),
-            function (Builder $query) use ($isMultiple, $values) {
-                if ($this->modifyRelationshipQueryUsing) {
-                    $query = $this->evaluate($this->modifyRelationshipQueryUsing, [
-                        'query' => $query,
-                    ]) ?? $query;
-                }
+        $filteredValues = $this->getRelationshipQueryValues($values);
 
-                if ($relationshipKey = $this->getRelationshipKey($query)) {
-                    return $query->{$isMultiple ? 'whereIn' : 'where'}(
-                        $relationshipKey,
-                        $values,
-                    );
-                }
+        $applyRelationshipScope = function (Builder $query) use ($isMultiple, $filteredValues): void {
+            if (empty($filteredValues)) {
+                return;
+            }
 
-                return $query->whereKey($values);
-            },
-        );
+            $query->whereHas(
+                $this->getRelationshipName(),
+                function (Builder $query) use ($isMultiple, $filteredValues): void {
+                    if ($this->modifyRelationshipQueryUsing) {
+                        $query = $this->evaluate($this->modifyRelationshipQueryUsing, [
+                            'query' => $query,
+                        ]) ?? $query;
+                    }
+
+                    $queryValues = $isMultiple ? $filteredValues : $filteredValues[0];
+
+                    if ($relationshipKey = $this->getRelationshipKey($query)) {
+                        $query->{$isMultiple ? 'whereIn' : 'where'}(
+                            $relationshipKey,
+                            $queryValues,
+                        );
+
+                        return;
+                    }
+
+                    $query->whereKey($queryValues);
+                },
+            );
+        };
 
         if (
             $this->hasEmptyRelationshipOption() &&
-            in_array('__empty', Arr::wrap($values))
+            in_array(static::EMPTY_RELATIONSHIP_OPTION_KEY, Arr::wrap($values))
         ) {
-            $query->where(fn (Builder $query) => $query
-                ->where(fn (Builder $query) => $applyRelationshipScope($query))
-                ->orWhereDoesntHave($this->getRelationshipName()));
+            if (filled($filteredValues)) {
+                $query
+                    ->where(fn (Builder $query) => $applyRelationshipScope($query))
+                    ->orWhereDoesntHave($this->getRelationshipName());
+            } else {
+                $query->whereDoesntHave($this->getRelationshipName());
+            }
         } else {
             $applyRelationshipScope($query);
         }
@@ -350,7 +368,7 @@ public function getFormField(): Select
                         $this->hasEmptyRelationshipOption() &&
                         str($this->getEmptyRelationshipOptionLabel())->lower()->contains(Str::lower($search))
                     ) {
-                        $options['__empty'] = $this->getEmptyRelationshipOptionLabel();
+                        $options[static::EMPTY_RELATIONSHIP_OPTION_KEY] = $this->getEmptyRelationshipOptionLabel();
                     }
 
                     $qualifiedRelatedKeyName = $component->getQualifiedRelatedKeyNameForRelationship($relationship);
@@ -416,7 +434,7 @@ public function getFormField(): Select
                     $options = [];
 
                     if ($this->hasEmptyRelationshipOption()) {
-                        $options['__empty'] = $this->getEmptyRelationshipOptionLabel();
+                        $options[static::EMPTY_RELATIONSHIP_OPTION_KEY] = $this->getEmptyRelationshipOptionLabel();
                     }
 
                     $qualifiedRelatedKeyName = $component->getQualifiedRelatedKeyNameForRelationship($relationship);
@@ -457,7 +475,7 @@ public function getFormField(): Select
                 ->getOptionLabelUsing(function (Select $component) {
                     if (
                         $this->hasEmptyRelationshipOption() &&
-                        ($component->getState() === '__empty')
+                        ($component->getState() === static::EMPTY_RELATIONSHIP_OPTION_KEY)
                     ) {
                         return $this->getEmptyRelationshipOptionLabel();
                     }
@@ -487,7 +505,7 @@ public function getFormField(): Select
 
                     $qualifiedRelatedKeyName = $component->getQualifiedRelatedKeyNameForRelationship($relationship);
 
-                    $relationshipQuery->whereIn($qualifiedRelatedKeyName, $values);
+                    $relationshipQuery->whereIn($qualifiedRelatedKeyName, $this->getRelationshipQueryValues($values));
 
                     if ($this->modifyRelationshipQueryUsing) {
                         $relationshipQuery = $component->evaluate($this->modifyRelationshipQueryUsing, [
@@ -500,9 +518,9 @@ public function getFormField(): Select
 
                     if (
                         $this->hasEmptyRelationshipOption() &&
-                        in_array('__empty', $values)
+                        in_array(static::EMPTY_RELATIONSHIP_OPTION_KEY, $values)
                     ) {
-                        $labels['__empty'] = $this->getEmptyRelationshipOptionLabel();
+                        $labels[static::EMPTY_RELATIONSHIP_OPTION_KEY] = $this->getEmptyRelationshipOptionLabel();
                     }
 
                     if ($component->hasOptionLabelFromRecordUsingCallback()) {
@@ -604,4 +622,16 @@ public function getOptionLabelFromRecordUsing(?Closure $callback): static
 
         return $this;
     }
+
+    /**
+     * @param  string | array<string>  $values
+     * @return array<string>
+     */
+    protected function getRelationshipQueryValues(string | array $values): array
+    {
+        return array_values(array_filter(
+            Arr::wrap($values),
+            fn (string $value): bool => $value !== static::EMPTY_RELATIONSHIP_OPTION_KEY,
+        ));
+    }
 }
diff --git a/tests/src/Fixtures/Livewire/PostsTableWithEmptyRelationshipFilter.php b/tests/src/Fixtures/Livewire/PostsTableWithEmptyRelationshipFilter.php
new file mode 100644
index 00000000000..73122659a0a
--- /dev/null
+++ b/tests/src/Fixtures/Livewire/PostsTableWithEmptyRelationshipFilter.php
@@ -0,0 +1,39 @@
+<?php
+
+namespace Filament\Tests\Fixtures\Livewire;
+
+use Filament\Actions\Concerns\InteractsWithActions;
+use Filament\Actions\Contracts\HasActions;
+use Filament\Schemas\Concerns\InteractsWithSchemas;
+use Filament\Schemas\Contracts\HasSchemas;
+use Filament\Tables;
+use Filament\Tables\Table;
+use Filament\Tests\Fixtures\Models\Post;
+use Illuminate\Contracts\View\View;
+use Livewire\Component;
+
+class PostsTableWithEmptyRelationshipFilter extends Component implements HasActions, HasSchemas, Tables\Contracts\HasTable
+{
+    use InteractsWithActions;
+    use InteractsWithSchemas;
+    use Tables\Concerns\InteractsWithTable;
+
+    public function table(Table $table): Table
+    {
+        return $table
+            ->query(Post::query())
+            ->columns([
+                Tables\Columns\TextColumn::make('title'),
+                Tables\Columns\TextColumn::make('author.name'),
+            ])
+            ->filters([
+                Tables\Filters\SelectFilter::make('author')
+                    ->relationship('author', 'name', hasEmptyOption: true),
+            ]);
+    }
+
+    public function render(): View
+    {
+        return view('livewire.table');
+    }
+}
diff --git a/tests/src/Fixtures/Livewire/PostsTableWithMultipleEmptyRelationshipFilter.php b/tests/src/Fixtures/Livewire/PostsTableWithMultipleEmptyRelationshipFilter.php
new file mode 100644
index 00000000000..305db89d302
--- /dev/null
+++ b/tests/src/Fixtures/Livewire/PostsTableWithMultipleEmptyRelationshipFilter.php
@@ -0,0 +1,40 @@
+<?php
+
+namespace Filament\Tests\Fixtures\Livewire;
+
+use Filament\Actions\Concerns\InteractsWithActions;
+use Filament\Actions\Contracts\HasActions;
+use Filament\Schemas\Concerns\InteractsWithSchemas;
+use Filament\Schemas\Contracts\HasSchemas;
+use Filament\Tables;
+use Filament\Tables\Table;
+use Filament\Tests\Fixtures\Models\Post;
+use Illuminate\Contracts\View\View;
+use Livewire\Component;
+
+class PostsTableWithMultipleEmptyRelationshipFilter extends Component implements HasActions, HasSchemas, Tables\Contracts\HasTable
+{
+    use InteractsWithActions;
+    use InteractsWithSchemas;
+    use Tables\Concerns\InteractsWithTable;
+
+    public function table(Table $table): Table
+    {
+        return $table
+            ->query(Post::query())
+            ->columns([
+                Tables\Columns\TextColumn::make('title'),
+                Tables\Columns\TextColumn::make('author.name'),
+            ])
+            ->filters([
+                Tables\Filters\SelectFilter::make('author')
+                    ->relationship('author', 'name', hasEmptyOption: true)
+                    ->multiple(),
+            ]);
+    }
+
+    public function render(): View
+    {
+        return view('livewire.table');
+    }
+}
diff --git a/tests/src/Tables/Filters/SelectFilterTest.php b/tests/src/Tables/Filters/SelectFilterTest.php
new file mode 100644
index 00000000000..6437ad80c75
--- /dev/null
+++ b/tests/src/Tables/Filters/SelectFilterTest.php
@@ -0,0 +1,86 @@
+<?php
+
+use Filament\Tests\Fixtures\Livewire\PostsTableWithEmptyRelationshipFilter;
+use Filament\Tests\Fixtures\Livewire\PostsTableWithMultipleEmptyRelationshipFilter;
+use Filament\Tests\Fixtures\Models\Post;
+use Filament\Tests\Fixtures\Models\User;
+use Filament\Tests\Tables\TestCase;
+
+use function Filament\Tests\livewire;
+
+uses(TestCase::class);
+
+it('can filter records with no relationship using `hasEmptyRelationshipOption`', function (): void {
+    $author = User::factory()->create();
+
+    $postsWithAuthor = Post::factory()->count(3)->create(['author_id' => $author->getKey()]);
+    $postsWithoutAuthor = Post::factory()->count(2)->create(['author_id' => null]);
+
+    livewire(PostsTableWithEmptyRelationshipFilter::class)
+        ->assertCanSeeTableRecords($postsWithAuthor->merge($postsWithoutAuthor))
+        ->filterTable('author', '__empty')
+        ->assertCanSeeTableRecords($postsWithoutAuthor)
+        ->assertCanNotSeeTableRecords($postsWithAuthor);
+});
+
+it('can filter records by specific relationship value using `hasEmptyRelationshipOption`', function (): void {
+    $author1 = User::factory()->create();
+    $author2 = User::factory()->create();
+
+    $postsWithAuthor1 = Post::factory()->count(3)->create(['author_id' => $author1->getKey()]);
+    $postsWithAuthor2 = Post::factory()->count(2)->create(['author_id' => $author2->getKey()]);
+    $postsWithoutAuthor = Post::factory()->count(2)->create(['author_id' => null]);
+
+    livewire(PostsTableWithEmptyRelationshipFilter::class)
+        ->assertCanSeeTableRecords($postsWithAuthor1->merge($postsWithAuthor2)->merge($postsWithoutAuthor))
+        ->filterTable('author', $author1->getKey())
+        ->assertCanSeeTableRecords($postsWithAuthor1)
+        ->assertCanNotSeeTableRecords($postsWithAuthor2)
+        ->assertCanNotSeeTableRecords($postsWithoutAuthor);
+});
+
+it('can filter records with no relationship using `hasEmptyRelationshipOption` with `multiple()`', function (): void {
+    $author = User::factory()->create();
+
+    $postsWithAuthor = Post::factory()->count(3)->create(['author_id' => $author->getKey()]);
+    $postsWithoutAuthor = Post::factory()->count(2)->create(['author_id' => null]);
+
+    livewire(PostsTableWithMultipleEmptyRelationshipFilter::class)
+        ->assertCanSeeTableRecords($postsWithAuthor->merge($postsWithoutAuthor))
+        ->filterTable('author', ['__empty'])
+        ->assertCanSeeTableRecords($postsWithoutAuthor)
+        ->assertCanNotSeeTableRecords($postsWithAuthor);
+});
+
+it('can filter records by specific relationship values using `hasEmptyRelationshipOption` with `multiple()`', function (): void {
+    $author1 = User::factory()->create();
+    $author2 = User::factory()->create();
+    $author3 = User::factory()->create();
+
+    $postsWithAuthor1 = Post::factory()->count(2)->create(['author_id' => $author1->getKey()]);
+    $postsWithAuthor2 = Post::factory()->count(2)->create(['author_id' => $author2->getKey()]);
+    $postsWithAuthor3 = Post::factory()->count(2)->create(['author_id' => $author3->getKey()]);
+    $postsWithoutAuthor = Post::factory()->count(2)->create(['author_id' => null]);
+
+    livewire(PostsTableWithMultipleEmptyRelationshipFilter::class)
+        ->assertCanSeeTableRecords($postsWithAuthor1->merge($postsWithAuthor2)->merge($postsWithAuthor3)->merge($postsWithoutAuthor))
+        ->filterTable('author', [$author1->getKey(), $author2->getKey()])
+        ->assertCanSeeTableRecords($postsWithAuthor1->merge($postsWithAuthor2))
+        ->assertCanNotSeeTableRecords($postsWithAuthor3)
+        ->assertCanNotSeeTableRecords($postsWithoutAuthor);
+});
+
+it('can filter records by relationship values combined with empty option using `hasEmptyRelationshipOption` with `multiple()`', function (): void {
+    $author1 = User::factory()->create();
+    $author2 = User::factory()->create();
+
+    $postsWithAuthor1 = Post::factory()->count(2)->create(['author_id' => $author1->getKey()]);
+    $postsWithAuthor2 = Post::factory()->count(2)->create(['author_id' => $author2->getKey()]);
+    $postsWithoutAuthor = Post::factory()->count(2)->create(['author_id' => null]);
+
+    livewire(PostsTableWithMultipleEmptyRelationshipFilter::class)
+        ->assertCanSeeTableRecords($postsWithAuthor1->merge($postsWithAuthor2)->merge($postsWithoutAuthor))
+        ->filterTable('author', ['__empty', $author1->getKey()])
+        ->assertCanSeeTableRecords($postsWithAuthor1->merge($postsWithoutAuthor))
+        ->assertCanNotSeeTableRecords($postsWithAuthor2);
+});