diff --git a/CHANGELOG.md b/CHANGELOG.md
index 19eba34c6..d4ea0fc44 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -30,6 +30,8 @@ Note that since we don't clearly distinguish between a public and private interf
 - Fix `flipSided` for meshes
 - Add `label/auth_comp_id` to `StructureProperties.residue`
   - Previously, this has been only been present on `.atom` (since residue name can alter on per-atom basis), but this has been a bit confusing for the general use-case
+- Move canvas "checked background" logic to `canvas3d.ts` and only apply it when `transparentBackground` is on
+  - This prevents an ugly flicked during plugin initialization
 
 ## [v5.4.2] - 2025-12-07
 - Fix postprocessing issues with SSAO and outlines for large structures (#1387)
diff --git a/breaking-v6-changes.md b/breaking-v6-changes.md
new file mode 100644
index 000000000..7b469d9e0
--- /dev/null
+++ b/breaking-v6-changes.md
@@ -0,0 +1 @@
+- Remove `checkeredCanvasBackground` from `PluginContext` and `PluginContainer`
\ No newline at end of file
diff --git a/src/apps/viewer/app.ts b/src/apps/viewer/app.ts
index 50067d974..cd3b15b9b 100644
--- a/src/apps/viewer/app.ts
+++ b/src/apps/viewer/app.ts
@@ -83,6 +83,9 @@ export class Viewer {
         }
 
         const spec: PluginUISpec = {
+            canvas3d: {
+                ...defaultSpec.canvas3d,
+            },
             actions: defaultSpec.actions,
             behaviors: [
                 ...baseBehaviors,
diff --git a/src/apps/viewer/mvs.html b/src/apps/viewer/mvs.html
index bf997ae67..e6a798d01 100644
--- a/src/apps/viewer/mvs.html
+++ b/src/apps/viewer/mvs.html
@@ -6,12 +6,16 @@
         <link rel="icon" href="./favicon.ico" type="image/x-icon">
         <title>Mol* Viewer MolViewSpec Example</title>
         <style>
+            body {
+                background: #111318;
+            }
+
             #app {
                 position: absolute;
-                left: 100px;
-                top: 100px;
-                width: 800px;
-                height: 600px;
+                left: 0;
+                top: 0;
+                width: 100%;
+                height: 100%;
             }
 
             #controls {
@@ -23,7 +27,7 @@
                 left: 10px;
                 top: 10px;
                 z-index: 10;
-                background-color: black;
+                background-color: #111318;
                 padding: 10px;
                 color: white;
             }
@@ -96,7 +100,7 @@
                 })
 
                 builder.canvas({
-                    background_color: "black",
+                    background_color: "#111318",
                 })
 
                 structure.primitives()
diff --git a/src/mol-canvas3d/canvas3d.ts b/src/mol-canvas3d/canvas3d.ts
index a1e359d17..034f60b43 100644
--- a/src/mol-canvas3d/canvas3d.ts
+++ b/src/mol-canvas3d/canvas3d.ts
@@ -96,6 +96,7 @@ export const Canvas3DParams = {
     cameraResetDurationMs: PD.Numeric(250, { min: 0, max: 1000, step: 1 }, { description: 'The time it takes to reset the camera.' }),
     sceneRadiusFactor: PD.Numeric(1, { min: 1, max: 10, step: 0.1 }),
     transparentBackground: PD.Boolean(false),
+    checkeredTransparentBackground: PD.Boolean(false),
     dpoitIterations: PD.Numeric(2, { min: 1, max: 10, step: 1 }),
     pickPadding: PD.Numeric(3, { min: 0, max: 10, step: 1 }, { description: 'Extra pixels to around target to check in case target is empty.' }),
     userInteractionReleaseMs: PD.Numeric(250, { min: 0, max: 1000, step: 1 }, { description: 'The time before the user is not considered interacting anymore.' }),
@@ -405,6 +406,22 @@ const cancelAnimationFrame = typeof window !== 'undefined'
     ? window.cancelAnimationFrame
     : (handle: number) => clearImmediate(handle as unknown as NodeJS.Immediate);
 
+function syncCanvasBackground(canvas: HTMLCanvasElement, canvasProps: Canvas3DProps) {
+    if (canvasProps.transparentBackground && canvasProps.checkeredTransparentBackground) {
+        Object.assign(canvas.style, {
+            'background-image': 'linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%, lightgrey), linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%, lightgrey)',
+            'background-size': '60px 60px',
+            'background-position': '0 0, 30px 30px'
+        });
+    } else {
+        Object.assign(canvas.style, {
+            'background-image': '',
+            'background-size': '',
+            'background-position': ''
+        });
+    }
+}
+
 namespace Canvas3D {
     export interface HoverEvent { current: Representation.Loci, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys, page?: Vec2, position?: Vec3 }
     export interface DragEvent { current: Representation.Loci, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys, pageStart: Vec2, pageEnd: Vec2 }
@@ -435,6 +452,7 @@ namespace Canvas3D {
         let forceNextRender = false;
         let currentTime = 0;
 
+        syncCanvasBackground(canvas!, p);
         updateViewport();
         const scene = Scene.create(webgl, passes.draw.transparency, {
             dColorMarker: p.renderer.colorMarker,
@@ -1061,6 +1079,7 @@ namespace Canvas3D {
                 cameraResetDurationMs: p.cameraResetDurationMs,
                 sceneRadiusFactor: p.sceneRadiusFactor,
                 transparentBackground: p.transparentBackground,
+                checkeredTransparentBackground: p.checkeredTransparentBackground,
                 dpoitIterations: p.dpoitIterations,
                 pickPadding: p.pickPadding,
                 userInteractionReleaseMs: p.userInteractionReleaseMs,
@@ -1311,6 +1330,7 @@ namespace Canvas3D {
                 }
                 if (props.cameraResetDurationMs !== undefined) p.cameraResetDurationMs = props.cameraResetDurationMs;
                 if (props.transparentBackground !== undefined) p.transparentBackground = props.transparentBackground;
+                if (props.checkeredTransparentBackground !== undefined) p.checkeredTransparentBackground = props.checkeredTransparentBackground;
                 if (props.dpoitIterations !== undefined) p.dpoitIterations = props.dpoitIterations;
                 if (props.pickPadding !== undefined) {
                     p.pickPadding = props.pickPadding;
@@ -1357,6 +1377,12 @@ namespace Canvas3D {
                     p.camera.stereo.name = 'off';
                 }
 
+                if ('transparentBackground' in props
+                    || 'checkeredTransparentBackground' in props
+                    || (props.renderer && 'backgroundColor' in props.renderer)) {
+                    syncCanvasBackground(canvas!, p);
+                }
+
                 shaderManager.updateRequired(p);
                 if (!doNotRequestDraw) {
                     requestDraw();
diff --git a/src/mol-plugin-ui/skin/base/components/viewport.scss b/src/mol-plugin-ui/skin/base/components/viewport.scss
index 3e05c7c87..da1cd537a 100644
--- a/src/mol-plugin-ui/skin/base/components/viewport.scss
+++ b/src/mol-plugin-ui/skin/base/components/viewport.scss
@@ -22,27 +22,6 @@
         z-index: 1000;
     }
 
-    .msp-viewport-host3d {
-        position: absolute;
-        left: 0;
-        top: 0;
-        right: 0;
-        bottom: 0;
-        -webkit-user-select: none;
-        user-select: none;
-        -webkit-tap-highlight-color: rgba(0, 0, 0, 0);
-        -webkit-touch-callout: none;
-        touch-action: manipulation;
-
-        >canvas {
-            background-color: $default-background;
-            background-image: linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%, lightgrey),
-                linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%, lightgrey);
-            background-size: 60px 60px;
-            background-position: 0 0, 30px 30px;
-        }
-    }
-
     .msp-viewport-controls {
         position: absolute;
         right: $control-spacing;
diff --git a/src/mol-plugin/container.ts b/src/mol-plugin/container.ts
index 5a031750b..9433f63b5 100644
--- a/src/mol-plugin/container.ts
+++ b/src/mol-plugin/container.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2024-25 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
@@ -19,6 +19,10 @@ export class PluginContainer {
         this.parent.parentElement?.removeChild(this.parent);
     }
 
+    /**
+     * options.checkeredCanvasBackground has no effect. Use canvas3d.checkeredTransparentBackground instead.
+     * TODO: remove in v6
+     */
     constructor(public options?: { checkeredCanvasBackground?: boolean, canvas?: HTMLCanvasElement }) {
         const parent = document.createElement('div');
         Object.assign(parent.style, {
@@ -36,13 +40,6 @@ export class PluginContainer {
         let canvas = options?.canvas;
         if (!canvas) {
             canvas = document.createElement('canvas');
-            if (options?.checkeredCanvasBackground) {
-                Object.assign(canvas.style, {
-                    'background-image': 'linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%, lightgrey), linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%, lightgrey)',
-                    'background-size': '60px 60px',
-                    'background-position': '0 0, 30px 30px'
-                });
-            }
             parent.appendChild(canvas);
         }
 
diff --git a/src/mol-plugin/context.ts b/src/mol-plugin/context.ts
index 2afa3bee1..a380e96c4 100644
--- a/src/mol-plugin/context.ts
+++ b/src/mol-plugin/context.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -246,6 +246,9 @@ export class PluginContext {
         if (!this._initViewer(container.canvas, container.parent, options?.canvas3dContext)) {
             return false;
         }
+        if (options?.checkeredCanvasBackground) {
+            this.canvas3d?.setProps({ checkeredTransparentBackground: true });
+        }
         this.container = container;
         return true;
     }