diff --git a/pcsx2/GS/Renderers/HW/GSRendererHW.cpp b/pcsx2/GS/Renderers/HW/GSRendererHW.cpp
index fb595bdd8a..ebf01b1ce8 100644
--- a/pcsx2/GS/Renderers/HW/GSRendererHW.cpp
+++ b/pcsx2/GS/Renderers/HW/GSRendererHW.cpp
@@ -8037,6 +8037,14 @@ __ri void GSRendererHW::DrawPrims(GSTextureCache::Target* rt, GSTextureCache::Ta
 	m_conf.drawarea = m_channel_shuffle ? scissor : scissor.rintersect(ComputeBoundingBox(rtsize, rtscale));
 	m_conf.scissor = (DATE && !DATE_BARRIER) ? m_conf.drawarea : scissor;
 
+	// ComputeDrawlistGetSize expects the original index layout, so needs to be called before we modify it via HandleProvokingVertexFirst/SetupIA.
+	if (m_conf.require_full_barrier && (g_gs_device->Features().texture_barrier || g_gs_device->Features().multidraw_fb_copy))
+	{
+		ComputeDrawlistGetSize(rt->m_scale);
+		m_conf.drawlist = &m_drawlist;
+		m_conf.drawlist_bbox = &m_drawlist_bbox;
+	}
+
 	HandleProvokingVertexFirst();
 
 	SetupIA(rtscale, sx, sy, m_channel_shuffle_width != 0);
@@ -8125,13 +8133,6 @@ __ri void GSRendererHW::DrawPrims(GSTextureCache::Target* rt, GSTextureCache::Ta
 		m_conf.alpha_second_pass.enable = false;
 	}
 
-	if (m_conf.require_full_barrier && (g_gs_device->Features().texture_barrier || g_gs_device->Features().multidraw_fb_copy))
-	{
-		ComputeDrawlistGetSize(rt->m_scale);
-		m_conf.drawlist = &m_drawlist;
-		m_conf.drawlist_bbox = &m_drawlist_bbox;
-	}
-
 	if (!m_channel_shuffle_width)
 		g_gs_device->RenderHW(m_conf);
 	else