diff --git a/include/sway/tree/container.h b/include/sway/tree/container.h
index b3406bbe5..d3f0ab023 100644
--- a/include/sway/tree/container.h
+++ b/include/sway/tree/container.h
@@ -176,17 +176,10 @@ struct sway_container *container_parent(struct sway_container *container,
  * surface-local coordinates of the given layout coordinates if the container
  * is a view and the view contains a surface at those coordinates.
  */
-struct sway_container *container_at(struct sway_container *container,
-		double ox, double oy, struct wlr_surface **surface,
+struct sway_container *container_at(struct sway_container *workspace,
+		double lx, double ly, struct wlr_surface **surface,
 		double *sx, double *sy);
 
-/**
- * Same as container_at, but only checks floating views and expects coordinates
- * to be layout coordinates, as that's what floating views use.
- */
-struct sway_container *floating_container_at(double lx, double ly,
-		struct wlr_surface **surface, double *sx, double *sy);
-
 /**
  * Apply the function for each descendant of the container breadth first.
  */
diff --git a/sway/desktop/output.c b/sway/desktop/output.c
index f0f1603a9..d8b066789 100644
--- a/sway/desktop/output.c
+++ b/sway/desktop/output.c
@@ -69,6 +69,7 @@ struct render_data {
 	struct root_geometry root_geo;
 	struct sway_output *output;
 	pixman_region32_t *damage;
+	bool popups;
 	float alpha;
 };
 
@@ -232,9 +233,26 @@ damage_finish:
 	pixman_region32_fini(&damage);
 }
 
+static bool surface_is_popup(struct wlr_surface *surface) {
+	if (wlr_surface_is_xdg_surface(surface)) {
+		struct wlr_xdg_surface *xdg_surface =
+			wlr_xdg_surface_from_wlr_surface(surface);
+		return xdg_surface->role == WLR_XDG_SURFACE_ROLE_POPUP;
+	}
+	if (wlr_surface_is_xdg_surface_v6(surface)) {
+		struct wlr_xdg_surface_v6 *xdg_surface_v6 =
+			wlr_xdg_surface_v6_from_wlr_surface(surface);
+		return xdg_surface_v6->role == WLR_XDG_SURFACE_V6_ROLE_POPUP;
+	}
+	return false;
+}
+
 static void render_surface_iterator(struct wlr_surface *surface, int sx, int sy,
 		void *_data) {
 	struct render_data *data = _data;
+	if (data->popups != surface_is_popup(surface)) {
+		return;
+	}
 	struct wlr_output *wlr_output = data->output->wlr_output;
 	float rotation = data->root_geo.rotation;
 	pixman_region32_t *output_damage = data->damage;
@@ -337,14 +355,16 @@ static void premultiply_alpha(float color[4], float opacity) {
 }
 
 static void render_view_surfaces(struct sway_view *view,
-		struct sway_output *output, pixman_region32_t *damage, float alpha) {
+		struct sway_output *output, pixman_region32_t *damage, float alpha,
+		bool popups) {
 	struct render_data data = {
 		.output = output,
 		.damage = damage,
 		.alpha = alpha,
+		.popups = popups,
 	};
-	output_view_for_each_surface(
-			view, &data.root_geo, render_surface_iterator, &data);
+	output_view_for_each_surface(view, &data.root_geo,
+			render_surface_iterator, &data);
 }
 
 /**
@@ -353,7 +373,8 @@ static void render_view_surfaces(struct sway_view *view,
 static void render_view(struct sway_output *output, pixman_region32_t *damage,
 		struct sway_container *con, struct border_colors *colors) {
 	struct sway_view *view = con->sway_view;
-	render_view_surfaces(view, output, damage, view->swayc->alpha);
+
+	render_view_surfaces(view, output, damage, con->alpha, false);
 
 	struct wlr_box box;
 	float output_scale = output->wlr_output->scale;
@@ -903,10 +924,11 @@ static void render_output(struct sway_output *output, struct timespec *when,
 		}
 
 		// TODO: handle views smaller than the output
-		render_view_surfaces(
-				workspace->sway_workspace->fullscreen, output, damage, 1.0f);
+		struct sway_view *view = workspace->sway_workspace->fullscreen;
+		render_view_surfaces(view, output, damage, 1.0f, false);
+		render_view_surfaces(view, output, damage, 1.0f, true);
 
-		if (workspace->sway_workspace->fullscreen->type == SWAY_VIEW_XWAYLAND) {
+		if (view->type == SWAY_VIEW_XWAYLAND) {
 			render_unmanaged(output, damage,
 				&root_container.sway_root->xwayland_unmanaged);
 		}
@@ -930,6 +952,11 @@ static void render_output(struct sway_output *output, struct timespec *when,
 		render_container(output, damage, workspace, focus == workspace);
 		render_floating(output, damage);
 
+		focus = seat_get_focus_inactive(seat, &root_container);
+		if (focus && focus->type == C_VIEW) {
+			render_view_surfaces(focus->sway_view, output, damage, 1.0f, true);
+		}
+
 		render_unmanaged(output, damage,
 			&root_container.sway_root->xwayland_unmanaged);
 		render_layer(output, damage,
diff --git a/sway/input/cursor.c b/sway/input/cursor.c
index 944e35aac..7d245f60e 100644
--- a/sway/input/cursor.c
+++ b/sway/input/cursor.c
@@ -108,9 +108,6 @@ static struct sway_container *container_at_coords(
 	}
 
 	struct sway_container *c;
-	if ((c = floating_container_at(lx, ly, surface, sx, sy))) {
-		return c;
-	}
 	if ((c = container_at(ws, lx, ly, surface, sx, sy))) {
 		return c;
 	}
diff --git a/sway/tree/container.c b/sway/tree/container.c
index af55a54e7..46f584fbd 100644
--- a/sway/tree/container.c
+++ b/sway/tree/container.c
@@ -489,9 +489,9 @@ struct sway_container *container_parent(struct sway_container *container,
 	return container;
 }
 
-static struct sway_container *container_at_view(struct sway_container *swayc,
-		double lx, double ly,
-		struct wlr_surface **surface, double *sx, double *sy) {
+static struct sway_container *surface_at_view(struct sway_container *swayc,
+		double lx, double ly, struct wlr_surface **surface,
+		double *sx, double *sy) {
 	if (!sway_assert(swayc->type == C_VIEW, "Expected a view")) {
 		return NULL;
 	}
@@ -531,10 +531,15 @@ static struct sway_container *container_at_view(struct sway_container *swayc,
 		*sx = _sx;
 		*sy = _sy;
 		*surface = _surface;
+		return swayc;
 	}
-	return swayc;
+	return NULL;
 }
 
+static struct sway_container *container_at_container(
+		struct sway_container *parent, double lx, double ly,
+		struct wlr_surface **surface, double *sx, double *sy);
+
 /**
  * container_at for a container with layout L_TABBED.
  */
@@ -561,7 +566,7 @@ static struct sway_container *container_at_tabbed(struct sway_container *parent,
 	// Surfaces
 	struct sway_container *current = seat_get_active_child(seat, parent);
 
-	return container_at(current, lx, ly, surface, sx, sy);
+	return container_at_container(current, lx, ly, surface, sx, sy);
 }
 
 /**
@@ -586,11 +591,14 @@ static struct sway_container *container_at_stacked(
 	// Surfaces
 	struct sway_container *current = seat_get_active_child(seat, parent);
 
-	return container_at(current, lx, ly, surface, sx, sy);
+	return container_at_container(current, lx, ly, surface, sx, sy);
 }
 
 /**
- * container_at for a container with layout L_HORIZ or L_VERT.
+ * container_at for a container with layout L_HORIZ, L_VERT or L_FLOATING.
+ *
+ * Iterates the children, does a box check and descends into the child if it
+ * passes.
  */
 static struct sway_container *container_at_linear(struct sway_container *parent,
 		double lx, double ly,
@@ -604,21 +612,18 @@ static struct sway_container *container_at_linear(struct sway_container *parent,
 			.height = child->height,
 		};
 		if (wlr_box_contains_point(&box, lx, ly)) {
-			return container_at(child, lx, ly, surface, sx, sy);
+			return container_at_container(child, lx, ly, surface, sx, sy);
 		}
 	}
 	return NULL;
 }
 
-struct sway_container *container_at(struct sway_container *parent,
-		double lx, double ly,
+static struct sway_container *container_at_container(
+		struct sway_container *parent, double lx, double ly,
 		struct wlr_surface **surface, double *sx, double *sy) {
-	if (!sway_assert(parent->type >= C_WORKSPACE,
-				"Expected workspace or deeper")) {
-		return NULL;
-	}
 	if (parent->type == C_VIEW) {
-		return container_at_view(parent, lx, ly, surface, sx, sy);
+		surface_at_view(parent, lx, ly, surface, sx, sy);
+		return parent;
 	}
 	if (!parent->children->length) {
 		return NULL;
@@ -634,42 +639,81 @@ struct sway_container *container_at(struct sway_container *parent,
 		return container_at_stacked(parent, lx, ly, surface, sx, sy);
 	case L_FLOATING:
 		sway_assert(false, "Didn't expect to see floating here");
-		return NULL;
+		// We can recover from this situation
+		return container_at_linear(parent, lx, ly, surface, sx, sy);
 	case L_NONE:
 		return NULL;
 	}
-
 	return NULL;
 }
 
-struct sway_container *floating_container_at(double lx, double ly,
+/**
+ * Iterate all visible workspaces and run container_at for each floating
+ * container.
+ */
+static struct sway_container *floating_container_at(double lx, double ly,
 		struct wlr_surface **surface, double *sx, double *sy) {
 	for (int i = 0; i < root_container.children->length; ++i) {
 		struct sway_container *output = root_container.children->items[i];
 		for (int j = 0; j < output->children->length; ++j) {
-			struct sway_container *workspace = output->children->items[j];
-			struct sway_workspace *ws = workspace->sway_workspace;
-			if (!workspace_is_visible(workspace)) {
+			struct sway_container *ws = output->children->items[j];
+			if (!workspace_is_visible(ws)) {
 				continue;
 			}
-			for (int k = 0; k < ws->floating->children->length; ++k) {
-				struct sway_container *floater =
-					ws->floating->children->items[k];
-				struct wlr_box box = {
-					.x = floater->x,
-					.y = floater->y,
-					.width = floater->width,
-					.height = floater->height,
-				};
-				if (wlr_box_contains_point(&box, lx, ly)) {
-					return container_at(floater, lx, ly, surface, sx, sy);
-				}
+			struct sway_container *c = container_at_linear(
+					ws->sway_workspace->floating, lx, ly, surface, sx, sy);
+			if (c) {
+				return c;
 			}
 		}
 	}
 	return NULL;
 }
 
+static bool surface_is_popup(struct wlr_surface *surface) {
+	if (wlr_surface_is_xdg_surface(surface)) {
+		struct wlr_xdg_surface *xdg_surface =
+			wlr_xdg_surface_from_wlr_surface(surface);
+		return xdg_surface->role == WLR_XDG_SURFACE_ROLE_POPUP;
+	}
+	if (wlr_surface_is_xdg_surface_v6(surface)) {
+		struct wlr_xdg_surface_v6 *xdg_surface_v6 =
+			wlr_xdg_surface_v6_from_wlr_surface(surface);
+		return xdg_surface_v6->role == WLR_XDG_SURFACE_V6_ROLE_POPUP;
+	}
+	return false;
+}
+
+struct sway_container *container_at(struct sway_container *workspace,
+		double lx, double ly,
+		struct wlr_surface **surface, double *sx, double *sy) {
+	if (!sway_assert(workspace->type == C_WORKSPACE, "Expected a workspace")) {
+		return NULL;
+	}
+	struct sway_container *c;
+	// Focused view's popups
+	struct sway_seat *seat = input_manager_current_seat(input_manager);
+	struct sway_container *focus =
+		seat_get_focus_inactive(seat, &root_container);
+	if (focus && focus->type == C_VIEW) {
+		c = surface_at_view(focus, lx, ly, surface, sx, sy);
+		if (*surface && !surface_is_popup(*surface)) {
+			*surface = NULL;
+		} else if (c) {
+			return c;
+		}
+	}
+	// Floating
+	if ((c = floating_container_at(lx, ly, surface, sx, sy))) {
+		return c;
+	}
+	// Tiling
+	if ((c = container_at_container(workspace, lx, ly, surface, sx, sy))) {
+		return c;
+	}
+	return NULL;
+}
+
 void container_for_each_descendant_dfs(struct sway_container *container,
 		void (*f)(struct sway_container *container, void *data),
 		void *data) {