diff --git a/app/src/resources/runs/__tests__/useCloneRun.test.tsx b/app/src/resources/runs/__tests__/useCloneRun.test.tsx
index cf9de675f67..87971872ede 100644
--- a/app/src/resources/runs/__tests__/useCloneRun.test.tsx
+++ b/app/src/resources/runs/__tests__/useCloneRun.test.tsx
@@ -13,7 +13,7 @@ import { useCloneRun } from '../useCloneRun'
 import { useNotifyRunQuery } from '../useNotifyRunQuery'
 
 import type { FunctionComponent, ReactNode } from 'react'
-import type { HostConfig } from '@opentrons/api-client'
+import type { HostConfig, LabwareOffset } from '@opentrons/api-client'
 
 vi.mock('@opentrons/react-api-client')
 vi.mock('/app/resources/runs/useNotifyRunQuery')
@@ -21,6 +21,7 @@ vi.mock('/app/resources/runs/useNotifyRunQuery')
 const HOST_CONFIG: HostConfig = { hostname: 'localhost' }
 const RUN_ID_NO_RTP: string = 'run_id_no_rtp'
 const RUN_ID_RTP: string = 'run_id_rtp'
+const RUN_ID_DUPLICATE_OFFSETS: string = 'run_id_duplicate_offsets'
 
 describe('useCloneRun hook', () => {
   let wrapper: FunctionComponent<{ children: ReactNode }>
@@ -34,7 +35,13 @@ describe('useCloneRun hook', () => {
           data: {
             id: RUN_ID_NO_RTP,
             protocolId: 'protocolId',
-            labwareOffsets: 'someOffset',
+            labwareOffsets: [
+              {
+                definitionUri: 'uri1',
+                locationSequence: [1, 2],
+                offset: { x: 1, y: 1, z: 1 },
+              },
+            ],
             runTimeParameters: [
               {
                 type: 'int',
@@ -59,7 +66,13 @@ describe('useCloneRun hook', () => {
           data: {
             id: RUN_ID_RTP,
             protocolId: 'protocolId',
-            labwareOffsets: 'someOffset',
+            labwareOffsets: [
+              {
+                definitionUri: 'uri1',
+                locationSequence: [1, 2],
+                offset: { x: 1, y: 1, z: 1 },
+              },
+            ],
             runTimeParameters: [
               {
                 type: 'int',
@@ -82,6 +95,38 @@ describe('useCloneRun hook', () => {
           },
         },
       } as any)
+
+    const duplicateOffsets: LabwareOffset[] = [
+      {
+        definitionUri: 'uri1',
+        locationSequence: [1, 2],
+        offset: { x: 1, y: 1, z: 1 },
+      },
+      {
+        definitionUri: 'uri2',
+        locationSequence: [3, 4],
+        offset: { x: 2, y: 2, z: 2 },
+      },
+      {
+        definitionUri: 'uri1',
+        locationSequence: [1, 2],
+        offset: { x: 3, y: 3, z: 3 },
+      },
+    ] as any
+
+    when(vi.mocked(useNotifyRunQuery))
+      .calledWith(RUN_ID_DUPLICATE_OFFSETS)
+      .thenReturn({
+        data: {
+          data: {
+            id: RUN_ID_DUPLICATE_OFFSETS,
+            protocolId: 'protocolId',
+            labwareOffsets: duplicateOffsets,
+            runTimeParameters: [],
+          },
+        },
+      } as any)
+
     when(vi.mocked(useCreateRunMutation))
       .calledWith(expect.anything())
       .thenReturn({ createRun: vi.fn() } as any)
@@ -111,11 +156,18 @@ describe('useCloneRun hook', () => {
     result.current && result.current.cloneRun()
     expect(mockCreateRun).toHaveBeenCalledWith({
       protocolId: 'protocolId',
-      labwareOffsets: 'someOffset',
+      labwareOffsets: [
+        {
+          definitionUri: 'uri1',
+          locationSequence: [1, 2],
+          offset: { x: 1, y: 1, z: 1 },
+        },
+      ],
       runTimeParameterValues: {},
       runTimeParameterFiles: {},
     })
   })
+
   it('should return a function that when called, calls createRun run with runTimeParameterValues overrides', async () => {
     const mockCreateRun = vi.fn()
     vi.mocked(useCreateRunMutation).mockReturnValue({
@@ -126,7 +178,74 @@ describe('useCloneRun hook', () => {
     result.current && result.current.cloneRun()
     expect(mockCreateRun).toHaveBeenCalledWith({
       protocolId: 'protocolId',
-      labwareOffsets: 'someOffset',
+      labwareOffsets: [
+        {
+          definitionUri: 'uri1',
+          locationSequence: [1, 2],
+          offset: { x: 1, y: 1, z: 1 },
+        },
+      ],
+      runTimeParameterValues: {
+        number_param: 2,
+        boolean_param: false,
+      },
+      runTimeParameterFiles: {
+        file_param: 'fileId_123',
+      },
+    })
+  })
+
+  it('should filter duplicate labware offsets and keep only the most recent ones', async () => {
+    const mockCreateRun = vi.fn()
+    vi.mocked(useCreateRunMutation).mockReturnValue({
+      createRun: mockCreateRun,
+    } as any)
+
+    const { result } = renderHook(() => useCloneRun(RUN_ID_DUPLICATE_OFFSETS), {
+      wrapper,
+    })
+    result.current && result.current.cloneRun()
+
+    const expectedOffsets = [
+      {
+        definitionUri: 'uri2',
+        locationSequence: [3, 4],
+        offset: { x: 2, y: 2, z: 2 },
+      },
+      {
+        definitionUri: 'uri1',
+        locationSequence: [1, 2],
+        offset: { x: 3, y: 3, z: 3 },
+      },
+    ]
+
+    expect(mockCreateRun).toHaveBeenCalledWith({
+      protocolId: 'protocolId',
+      labwareOffsets: expectedOffsets,
+      runTimeParameterValues: {},
+      runTimeParameterFiles: {},
+    })
+  })
+
+  it('should handle analysis trigger when specified', async () => {
+    const mockCreateRun = vi.fn()
+    const mockCreateProtocolAnalysis = vi.fn()
+
+    vi.mocked(useCreateRunMutation).mockReturnValue({
+      createRun: mockCreateRun,
+    } as any)
+    vi.mocked(useCreateProtocolAnalysisMutation).mockReturnValue({
+      createProtocolAnalysis: mockCreateProtocolAnalysis,
+    } as any)
+
+    const { result } = renderHook(
+      () => useCloneRun(RUN_ID_RTP, undefined, true),
+      { wrapper }
+    )
+    result.current && result.current.cloneRun()
+
+    expect(mockCreateProtocolAnalysis).toHaveBeenCalledWith({
+      protocolKey: 'protocolId',
       runTimeParameterValues: {
         number_param: 2,
         boolean_param: false,
diff --git a/app/src/resources/runs/useCloneRun.ts b/app/src/resources/runs/useCloneRun.ts
index 45f3a7a2c67..5dd3fdc9a4c 100644
--- a/app/src/resources/runs/useCloneRun.ts
+++ b/app/src/resources/runs/useCloneRun.ts
@@ -11,7 +11,8 @@ import {
   getRunTimeParameterFilesForRun,
 } from '/app/transformations/runs'
 
-import type { Run } from '@opentrons/api-client'
+import type { LabwareOffset, Run } from '@opentrons/api-client'
+import isEqual from 'lodash/isEqual'
 
 interface UseCloneRunResult {
   cloneRun: () => void
@@ -70,7 +71,7 @@ export function useCloneRun(
       }
       createRun({
         protocolId,
-        labwareOffsets,
+        labwareOffsets: mostRecentUniqueLabwareOffsets(labwareOffsets),
         runTimeParameterValues,
         runTimeParameterFiles,
       })
@@ -81,3 +82,19 @@ export function useCloneRun(
 
   return { cloneRun, isLoadingRun, isCloning }
 }
+
+// Returns the most recent, unique offsets for each labware uri + location pair.
+// Assumes the most recent labware offsets are appended to the end of the list.
+function mostRecentUniqueLabwareOffsets(
+  offsets: LabwareOffset[] | undefined
+): LabwareOffset[] | undefined {
+  return offsets?.filter((offset, index, array) => {
+    return (
+      array.findLastIndex(
+        firstOffset =>
+          isEqual(firstOffset.locationSequence, offset.locationSequence) &&
+          isEqual(firstOffset.definitionUri, offset.definitionUri)
+      ) === index
+    )
+  })
+}