diff --git a/src/amd/vulkan/nir/radv_nir_lower_io.c b/src/amd/vulkan/nir/radv_nir_lower_io.c
index 5cd6f0b4b4d..6fb7e4fa124 100644
--- a/src/amd/vulkan/nir/radv_nir_lower_io.c
+++ b/src/amd/vulkan/nir/radv_nir_lower_io.c
@@ -113,13 +113,13 @@ radv_recompute_fs_input_bases_callback(UNUSED nir_builder *b, nir_intrinsic_inst
 bool
 radv_recompute_fs_input_bases(nir_shader *nir)
 {
-   const uint64_t always_per_vertex =
-      nir->info.inputs_read & ~nir->info.per_primitive_inputs & ~(VARYING_BIT_PRIMITIVE_ID | VARYING_BIT_VIEWPORT);
+   const uint64_t always_per_vertex = nir->info.inputs_read & ~nir->info.per_primitive_inputs &
+                                      ~(VARYING_BIT_PRIMITIVE_ID | VARYING_BIT_VIEWPORT | VARYING_BIT_LAYER);
 
    const uint64_t potentially_per_primitive = nir->info.inputs_read & (VARYING_BIT_PRIMITIVE_ID | VARYING_BIT_VIEWPORT);
 
-   const uint64_t always_per_primitive =
-      nir->info.inputs_read & nir->info.per_primitive_inputs & ~(VARYING_BIT_PRIMITIVE_ID | VARYING_BIT_VIEWPORT);
+   const uint64_t always_per_primitive = nir->info.inputs_read & nir->info.per_primitive_inputs &
+                                         ~(VARYING_BIT_PRIMITIVE_ID | VARYING_BIT_VIEWPORT | VARYING_BIT_LAYER);
 
    radv_recompute_fs_input_bases_state s = {
       .always_per_vertex = always_per_vertex,
diff --git a/src/gallium/drivers/zink/ci/zink-radv-navi10-flakes.txt b/src/gallium/drivers/zink/ci/zink-radv-navi10-flakes.txt
index 1f6b7b0d3e6..834b2a1b5b5 100644
--- a/src/gallium/drivers/zink/ci/zink-radv-navi10-flakes.txt
+++ b/src/gallium/drivers/zink/ci/zink-radv-navi10-flakes.txt
@@ -44,6 +44,3 @@ KHR-GL46.sparse_buffer_tests.BufferStorageTest
 dEQP-GLES3.functional.fbo.multiview.samples_4
 spec@glsl-1.50@execution@redeclare-pervertex-out-subset-gs
 dEQP-GLES31.functional.synchronization.inter_call.without_memory_barrier.ssbo_atomic_counter_mixed_dispatch_100_calls_128_invocations
-
-# https://gitlab.freedesktop.org/mesa/mesa/-/issues/12501
-spec@arb_fragment_layer_viewport@layer-gs-writes-in-range
diff --git a/src/gallium/drivers/zink/ci/zink-radv-navi31-flakes.txt b/src/gallium/drivers/zink/ci/zink-radv-navi31-flakes.txt
index a016d0de4c4..efe712f34b3 100644
--- a/src/gallium/drivers/zink/ci/zink-radv-navi31-flakes.txt
+++ b/src/gallium/drivers/zink/ci/zink-radv-navi31-flakes.txt
@@ -59,6 +59,3 @@ spec@glsl-1.50@execution@redeclare-pervertex-out-subset-gs
 
 # First seen on navi10 in https://gitlab.freedesktop.org/mesa/mesa/-/jobs/58636780
 KHR-GL46.sparse_buffer_tests.BufferStorageTest
-
-# https://gitlab.freedesktop.org/mesa/mesa/-/issues/12501
-spec@arb_fragment_layer_viewport@layer-gs-writes-in-range
diff --git a/src/gallium/drivers/zink/ci/zink-radv-polaris10-flakes.txt b/src/gallium/drivers/zink/ci/zink-radv-polaris10-flakes.txt
index 044287e4e48..89f6ab5d212 100644
--- a/src/gallium/drivers/zink/ci/zink-radv-polaris10-flakes.txt
+++ b/src/gallium/drivers/zink/ci/zink-radv-polaris10-flakes.txt
@@ -50,6 +50,3 @@ spec@arb_query_buffer_object@coherency@indirect-draw-GL_GEOMETRY_SHADER_PRIMITIV
 spec@arb_query_buffer_object@coherency@indirect-draw-count-GL_GEOMETRY_SHADER_INVOCATIONS
 spec@arb_query_buffer_object@coherency@indirect-draw-count-GL_GEOMETRY_SHADER_PRIMITIVES_EMITTED
 spec@ext_timer_query@time-elapsed
-
-# https://gitlab.freedesktop.org/mesa/mesa/-/issues/12501
-spec@arb_fragment_layer_viewport@layer-gs-writes-in-range
diff --git a/src/gallium/drivers/zink/ci/zink-radv-vangogh-flakes.txt b/src/gallium/drivers/zink/ci/zink-radv-vangogh-flakes.txt
index a61b736acf3..5a58724ac97 100644
--- a/src/gallium/drivers/zink/ci/zink-radv-vangogh-flakes.txt
+++ b/src/gallium/drivers/zink/ci/zink-radv-vangogh-flakes.txt
@@ -103,6 +103,3 @@ dEQP-GLES31.functional.copy_image.mixed.viewclass_64_bits_mixed.rg32f_r11_eac.te
 dEQP-GLES31.functional.draw_indirect.compute_interop.large.drawelements_separate_grid_100x100_drawcount_200
 dEQP-GLES31.functional.draw_indirect.compute_interop.large.drawelements_separate_grid_1200x1200_drawcount_1
 spec@arb_compute_shader@zero-dispatch-size
-
-# https://gitlab.freedesktop.org/mesa/mesa/-/issues/12501
-spec@arb_fragment_layer_viewport@layer-gs-writes-in-range