diff --git a/protocol-designer/src/pages/Designer/DeckSetup/DeckSetupTools.tsx b/protocol-designer/src/pages/Designer/DeckSetup/DeckSetupTools.tsx
index 62a5f92d46e..44732c1e0ed 100644
--- a/protocol-designer/src/pages/Designer/DeckSetup/DeckSetupTools.tsx
+++ b/protocol-designer/src/pages/Designer/DeckSetup/DeckSetupTools.tsx
@@ -18,6 +18,7 @@ import {
 } from '@opentrons/components'
 import {
   FLEX_ROBOT_TYPE,
+  FLEX_STAGING_AREA_SLOT_ADDRESSABLE_AREAS,
   getModuleDisplayName,
   getModuleType,
   MAGNETIC_MODULE_TYPE,
@@ -58,7 +59,7 @@ import { LabwareTools } from './LabwareTools'
 import { MagnetModuleChangeContent } from './MagnetModuleChangeContent'
 import { getModuleModelsBySlot, getDeckErrors } from './utils'
 
-import type { ModuleModel } from '@opentrons/shared-data'
+import type { AddressableAreaName, ModuleModel } from '@opentrons/shared-data'
 import type { ThunkDispatch } from '../../../types'
 import type { Fixture } from './constants'
 
@@ -242,7 +243,7 @@ export function DeckSetupTools(props: DeckSetupToolsProps): JSX.Element | null {
     handleResetSearchTerm()
   }
 
-  const handleClear = (): void => {
+  const handleClear = (keepExistingLabware = false): void => {
     onDeckProps?.setHoveredModule(null)
     onDeckProps?.setHoveredFixture(null)
     if (slot !== 'offDeck') {
@@ -250,31 +251,41 @@ export function DeckSetupTools(props: DeckSetupToolsProps): JSX.Element | null {
       if (createdModuleForSlot != null) {
         dispatch(deleteModule(createdModuleForSlot.id))
       }
-      //  clear fixture(s) from slot
-      if (createFixtureForSlots != null && createFixtureForSlots.length > 0) {
-        createFixtureForSlots.forEach(fixture =>
-          dispatch(deleteDeckFixture(fixture.id))
-        )
-      }
       //  clear labware from slot
       if (
         createdLabwareForSlot != null &&
-        createdLabwareForSlot.labwareDefURI !== selectedLabwareDefUri
+        (!keepExistingLabware ||
+          createdLabwareForSlot.labwareDefURI !== selectedLabwareDefUri)
       ) {
         dispatch(deleteContainer({ labwareId: createdLabwareForSlot.id }))
       }
       //  clear nested labware from slot
       if (
         createdNestedLabwareForSlot != null &&
-        createdNestedLabwareForSlot.labwareDefURI !==
-          selectedNestedLabwareDefUri
+        (!keepExistingLabware ||
+          createdNestedLabwareForSlot.labwareDefURI !==
+            selectedNestedLabwareDefUri)
       ) {
         dispatch(deleteContainer({ labwareId: createdNestedLabwareForSlot.id }))
       }
       // clear labware on staging area 4th column slot
-      if (matchingLabwareFor4thColumn != null) {
+      if (matchingLabwareFor4thColumn != null && !keepExistingLabware) {
         dispatch(deleteContainer({ labwareId: matchingLabwareFor4thColumn.id }))
       }
+      //  clear fixture(s) from slot
+      if (createFixtureForSlots != null && createFixtureForSlots.length > 0) {
+        createFixtureForSlots.forEach(fixture =>
+          dispatch(deleteDeckFixture(fixture.id))
+        )
+        // zoom out if you're clearing a staging area slot directly from a 4th column
+        if (
+          FLEX_STAGING_AREA_SLOT_ADDRESSABLE_AREAS.includes(
+            slot as AddressableAreaName
+          )
+        ) {
+          dispatch(selectZoomedIntoSlot({ slot: null, cutout: null }))
+        }
+      }
     }
     handleResetToolbox()
     handleResetLabwareTools()
@@ -285,7 +296,7 @@ export function DeckSetupTools(props: DeckSetupToolsProps): JSX.Element | null {
   }
   const handleConfirm = (): void => {
     //  clear entities first before recreating them
-    handleClear()
+    handleClear(true)
 
     if (selectedFixture != null && cutout != null) {
       //  create fixture(s)
diff --git a/protocol-designer/src/pages/Designer/DeckSetup/SlotOverflowMenu.tsx b/protocol-designer/src/pages/Designer/DeckSetup/SlotOverflowMenu.tsx
index 8cc15363ea6..c6c37c5be31 100644
--- a/protocol-designer/src/pages/Designer/DeckSetup/SlotOverflowMenu.tsx
+++ b/protocol-designer/src/pages/Designer/DeckSetup/SlotOverflowMenu.tsx
@@ -15,6 +15,12 @@ import {
   StyledText,
   useOnClickOutside,
 } from '@opentrons/components'
+import {
+  FLEX_ROBOT_TYPE,
+  FLEX_STAGING_AREA_SLOT_ADDRESSABLE_AREAS,
+  getCutoutIdFromAddressableArea,
+  getDeckDefFromRobotType,
+} from '@opentrons/shared-data'
 import { getDeckSetupForActiveItem } from '../../../top-selectors/labware-locations'
 
 import { deleteModule } from '../../../step-forms/actions'
@@ -32,10 +38,12 @@ import { getStagingAreaAddressableAreas } from '../../../utils'
 import { selectors as labwareIngredSelectors } from '../../../labware-ingred/selectors'
 import type { MouseEvent, SetStateAction } from 'react'
 import type {
+  AddressableAreaName,
   CoordinateTuple,
   CutoutId,
   DeckSlotId,
 } from '@opentrons/shared-data'
+
 import type { LabwareOnDeck } from '../../../step-forms'
 import type { ThunkDispatch } from '../../../types'
 
@@ -146,6 +154,10 @@ export function SlotOverflowMenu(
   const hasNoItems =
     moduleOnSlot == null && labwareOnSlot == null && fixturesOnSlot.length === 0
 
+  const isStagingSlot = FLEX_STAGING_AREA_SLOT_ADDRESSABLE_AREAS.includes(
+    location as AddressableAreaName
+  )
+
   const handleClear = (): void => {
     //  clear module from slot
     if (moduleOnSlot != null) {
@@ -167,6 +179,21 @@ export function SlotOverflowMenu(
     if (matchingLabware != null) {
       dispatch(deleteContainer({ labwareId: matchingLabware.id }))
     }
+    // delete staging slot if addressable area is on staging slot
+    if (isStagingSlot) {
+      const deckDef = getDeckDefFromRobotType(FLEX_ROBOT_TYPE)
+      const cutoutId = getCutoutIdFromAddressableArea(location, deckDef)
+      const stagingAreaEquipmentId = Object.values(
+        additionalEquipmentOnDeck
+      ).find(({ location }) => location === cutoutId)?.id
+      if (stagingAreaEquipmentId != null) {
+        dispatch(deleteDeckFixture(stagingAreaEquipmentId))
+      } else {
+        console.error(
+          `could not find equipment id for entity in ${location} with cutout id ${cutoutId}`
+        )
+      }
+    }
   }
 
   const showDuplicateBtn =
@@ -303,7 +330,7 @@ export function SlotOverflowMenu(
         ) : null}
         <Divider marginY="0" />
         <MenuItem
-          disabled={hasNoItems}
+          disabled={hasNoItems && !isStagingSlot}
           onClick={(e: MouseEvent) => {
             if (matchingLabware != null) {
               setShowDeleteLabwareModal(true)
diff --git a/protocol-designer/src/pages/Designer/DeckSetup/__tests__/DeckSetupTools.test.tsx b/protocol-designer/src/pages/Designer/DeckSetup/__tests__/DeckSetupTools.test.tsx
index 5371faed57c..5eab480710e 100644
--- a/protocol-designer/src/pages/Designer/DeckSetup/__tests__/DeckSetupTools.test.tsx
+++ b/protocol-designer/src/pages/Designer/DeckSetup/__tests__/DeckSetupTools.test.tsx
@@ -1,4 +1,4 @@
-import { describe, it, expect, vi, beforeEach } from 'vitest'
+import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest'
 import '@testing-library/jest-dom/vitest'
 import { fireEvent, screen } from '@testing-library/react'
 import {
@@ -67,6 +67,9 @@ describe('DeckSetupTools', () => {
     })
     vi.mocked(getDismissedHints).mockReturnValue([])
   })
+  afterEach(() => {
+    vi.resetAllMocks()
+  })
   it('should render the relevant modules and fixtures for slot D3 on Flex with tabs', () => {
     render(props)
     screen.getByText('Add a module')
@@ -92,6 +95,14 @@ describe('DeckSetupTools', () => {
     screen.getByText('mock labware tools')
   })
   it('should clear the slot from all items when the clear cta is called', () => {
+    vi.mocked(selectors.getZoomedInSlotInfo).mockReturnValue({
+      selectedLabwareDefUri: 'mockUri',
+      selectedNestedLabwareDefUri: 'mockUri',
+      selectedFixture: null,
+      selectedModuleModel: null,
+      selectedSlot: { slot: 'D3', cutout: 'cutoutD3' },
+    })
+
     vi.mocked(getDeckSetupForActiveItem).mockReturnValue({
       labware: {
         labId: {
diff --git a/protocol-designer/src/pages/Designer/DeckSetup/__tests__/SlotOverflowMenu.test.tsx b/protocol-designer/src/pages/Designer/DeckSetup/__tests__/SlotOverflowMenu.test.tsx
index 2ba0d4df60f..56d5af2f806 100644
--- a/protocol-designer/src/pages/Designer/DeckSetup/__tests__/SlotOverflowMenu.test.tsx
+++ b/protocol-designer/src/pages/Designer/DeckSetup/__tests__/SlotOverflowMenu.test.tsx
@@ -1,5 +1,5 @@
 import type * as React from 'react'
-import { describe, it, expect, vi, beforeEach } from 'vitest'
+import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest'
 import '@testing-library/jest-dom/vitest'
 import { fireEvent, screen } from '@testing-library/react'
 import { fixture96Plate } from '@opentrons/shared-data'
@@ -42,6 +42,8 @@ const render = (props: React.ComponentProps<typeof SlotOverflowMenu>) => {
   })[0]
 }
 
+const MOCK_STAGING_AREA_ID = 'MOCK_STAGING_AREA_ID'
+
 describe('SlotOverflowMenu', () => {
   let props: React.ComponentProps<typeof SlotOverflowMenu>
 
@@ -78,7 +80,11 @@ describe('SlotOverflowMenu', () => {
         },
       },
       additionalEquipmentOnDeck: {
-        fixture: { name: 'stagingArea', id: 'mockId', location: 'cutoutD3' },
+        fixture: {
+          name: 'stagingArea',
+          id: MOCK_STAGING_AREA_ID,
+          location: 'cutoutD3',
+        },
       },
     })
     vi.mocked(EditNickNameModal).mockReturnValue(
@@ -87,6 +93,10 @@ describe('SlotOverflowMenu', () => {
     vi.mocked(labwareIngredSelectors.getLiquidsByLabwareId).mockReturnValue({})
   })
 
+  afterEach(() => {
+    vi.restoreAllMocks()
+  })
+
   it('should renders all buttons as enabled and clicking on them calls ctas', () => {
     render(props)
     fireEvent.click(
@@ -134,4 +144,25 @@ describe('SlotOverflowMenu', () => {
     expect(mockNavigate).toHaveBeenCalled()
     expect(vi.mocked(openIngredientSelector)).toHaveBeenCalled()
   })
+  it('deletes the staging area slot and all labware and modules on top of it', () => {
+    vi.mocked(labwareIngredSelectors.getLiquidsByLabwareId).mockReturnValue({
+      labId2: { well1: { '0': { volume: 10 } } },
+    })
+    render(props)
+    fireEvent.click(screen.getByRole('button', { name: 'Clear slot' }))
+
+    expect(vi.mocked(deleteDeckFixture)).toHaveBeenCalledOnce()
+    expect(vi.mocked(deleteDeckFixture)).toHaveBeenCalledWith(
+      MOCK_STAGING_AREA_ID
+    )
+    expect(vi.mocked(deleteContainer)).toHaveBeenCalledTimes(2)
+    expect(vi.mocked(deleteContainer)).toHaveBeenNthCalledWith(1, {
+      labwareId: 'labId',
+    })
+    expect(vi.mocked(deleteContainer)).toHaveBeenNthCalledWith(2, {
+      labwareId: 'labId2',
+    })
+    expect(vi.mocked(deleteModule)).toHaveBeenCalledOnce()
+    expect(vi.mocked(deleteModule)).toHaveBeenCalledWith('modId')
+  })
 })
diff --git a/shared-data/js/helpers/index.ts b/shared-data/js/helpers/index.ts
index 4c3fde2c91e..57cb24e31ee 100644
--- a/shared-data/js/helpers/index.ts
+++ b/shared-data/js/helpers/index.ts
@@ -10,6 +10,7 @@ import type {
   RobotType,
   ThermalAdapterName,
 } from '../types'
+import type { AddressableAreaName, CutoutId } from '../../deck/types/schemaV5'
 
 export { getWellNamePerMultiTip } from './getWellNamePerMultiTip'
 export { getWellTotalVolume } from './getWellTotalVolume'
@@ -373,3 +374,28 @@ export const getDeckDefFromRobotType = (
     ? standardFlexDeckDef
     : standardOt2DeckDef
 }
+
+export const getCutoutIdFromAddressableArea = (
+  addressableAreaName: string,
+  deckDefinition: DeckDefinition
+): CutoutId | null => {
+  /**
+   * Given an addressable area name, returns the cutout ID associated with it, or null if there is none
+   */
+
+  for (const cutoutFixture of deckDefinition.cutoutFixtures) {
+    for (const [cutoutId, providedAreas] of Object.entries(
+      cutoutFixture.providesAddressableAreas
+    ) as Array<[CutoutId, AddressableAreaName[]]>) {
+      if (providedAreas.includes(addressableAreaName as AddressableAreaName)) {
+        return cutoutId
+      }
+    }
+  }
+
+  console.error(
+    `${addressableAreaName} is not provided by any cutout fixtures in deck definition ${deckDefinition.otId}`
+  )
+
+  return null
+}