diff --git a/pcsx2/GS/Renderers/HW/GSRendererHW.cpp b/pcsx2/GS/Renderers/HW/GSRendererHW.cpp
index 97bd390334a7e..c3b2eab17fe60 100644
--- a/pcsx2/GS/Renderers/HW/GSRendererHW.cpp
+++ b/pcsx2/GS/Renderers/HW/GSRendererHW.cpp
@@ -6002,12 +6002,12 @@ __ri void GSRendererHW::DrawPrims(GSTextureCache::Target* rt, GSTextureCache::Ta
 
 	// FIXME D3D11 and GL support half pixel center. Code could be easier!!!
 	const GSTextureCache::Target* rt_or_ds = rt ? rt : ds;
-	const float rtscale = rt_or_ds ? rt_or_ds->GetScale() : 0.0f;
-	const GSVector2i rtsize = rt_or_ds ? rt_or_ds->GetTexture()->GetSize() : GSVector2i(0, 0);
+	const float rtscale = rt_or_ds->GetScale();
+	const GSVector2i rtsize = rt_or_ds->GetTexture()->GetSize();
 	float sx, sy, ox2, oy2;
 	const float ox = static_cast<float>(static_cast<int>(m_context->XYOFFSET.OFX));
 	const float oy = static_cast<float>(static_cast<int>(m_context->XYOFFSET.OFY));
-	if (GSConfig.UserHacks_HalfPixelOffset != GSHalfPixelOffset::Native && (!rt || rt->GetScale() > 1.0f))
+	if (GSConfig.UserHacks_HalfPixelOffset != GSHalfPixelOffset::Native && rtscale > 1.0f)
 	{
 		sx = 2.0f * rtscale / (rtsize.x << 4);
 		sy = 2.0f * rtscale / (rtsize.y << 4);
@@ -6032,12 +6032,12 @@ __ri void GSRendererHW::DrawPrims(GSTextureCache::Target* rt, GSTextureCache::Ta
 	else
 	{
 		// Align coordinates to native resolution framebuffer, hope for the best.
-		const int scaled_x = rt_or_ds ? rt_or_ds->GetUnscaledWidth() : 0;
-		const int scaled_y = rt_or_ds ? rt_or_ds->GetUnscaledHeight() : 0;
-		sx = 2.0f / (scaled_x << 4);
-		sy = 2.0f / (scaled_y << 4);
-		ox2 = -1.0f / scaled_x;
-		oy2 = -1.0f / scaled_y;
+		const int unscaled_x = rt_or_ds ? rt_or_ds->GetUnscaledWidth() : 0;
+		const int unscaled_y = rt_or_ds ? rt_or_ds->GetUnscaledHeight() : 0;
+		sx = 2.0f / (unscaled_x << 4);
+		sy = 2.0f / (unscaled_y << 4);
+		ox2 = -1.0f / unscaled_x;
+		oy2 = -1.0f / unscaled_y;
 	}
 
 	m_conf.cb_vs.vertex_scale = GSVector2(sx, sy);
diff --git a/pcsx2/GS/Renderers/HW/GSTextureCache.cpp b/pcsx2/GS/Renderers/HW/GSTextureCache.cpp
index 3646ef1fc925f..55e0e0f92c109 100644
--- a/pcsx2/GS/Renderers/HW/GSTextureCache.cpp
+++ b/pcsx2/GS/Renderers/HW/GSTextureCache.cpp
@@ -2113,8 +2113,20 @@ GSTextureCache::Target* GSTextureCache::LookupTarget(GIFRegTEX0 TEX0, const GSVe
 				}
 
 				// And invalidate the target, we're drawing over it so we don't care what's there.
-				GL_INS("TC: Invalidating target %s[%x] because it's completely overwritten.", to_string(type), dst->m_TEX0.TBP0);
-				g_gs_device->InvalidateRenderTarget(dst->m_texture);
+				// We can't do this when upscaling, because of the vertex offset, the top/left rows often aren't drawn.
+				GL_INS("TC: Invalidating%s target %s[%x] because it's completely overwritten.", to_string(type),
+					(scale > 1.0f && GSConfig.UserHacks_HalfPixelOffset == GSHalfPixelOffset::Native) ? "[clearing] " : "", dst->m_TEX0.TBP0);
+				if (scale > 1.0f && GSConfig.UserHacks_HalfPixelOffset != GSHalfPixelOffset::Native)
+				{
+					if (dst->m_type == RenderTarget)
+						g_gs_device->ClearRenderTarget(dst->m_texture, 0);
+					else
+						g_gs_device->ClearDepth(dst->m_texture, 0.0f);
+				}
+				else
+				{
+					g_gs_device->InvalidateRenderTarget(dst->m_texture);
+				}
 			}
 		}
 	}
diff --git a/pcsx2/Pcsx2Config.cpp b/pcsx2/Pcsx2Config.cpp
index a79a10bd315bb..ccb179f7c3df4 100644
--- a/pcsx2/Pcsx2Config.cpp
+++ b/pcsx2/Pcsx2Config.cpp
@@ -884,7 +884,7 @@ void Pcsx2Config::GSOptions::LoadSave(SettingsWrapper& wrap)
 	SettingsWrapEntryEx(UpscaleMultiplier, "upscale_multiplier");
 
 	// ~51x would the upper bound here for 32768x32768 textures, but you'll run out VRAM long before then.
-	UpscaleMultiplier = std::clamp(UpscaleMultiplier, 0.5f, 50.0f);
+	UpscaleMultiplier = std::clamp(UpscaleMultiplier, 1.0f, 50.0f);
 
 	SettingsWrapBitBoolEx(HWMipmap, "hw_mipmap");
 	SettingsWrapIntEnumEx(AccurateBlendingUnit, "accurate_blending_unit");