diff --git a/src/plugins/vis_types/xy/public/config/get_config.test.ts b/src/plugins/vis_types/xy/public/config/get_config.test.ts
index 52d68b40766a90..7608ef7cda4608 100644
--- a/src/plugins/vis_types/xy/public/config/get_config.test.ts
+++ b/src/plugins/vis_types/xy/public/config/get_config.test.ts
@@ -7,7 +7,8 @@
  */
 
 import { getConfig } from './get_config';
-import { visData, visParamsWithTwoYAxes } from '../mocks';
+import { visData, visDataPercentile, visParamsWithTwoYAxes } from '../mocks';
+import { VisParams } from '../types';
 
 // ToDo: add more tests for all the config properties
 describe('getConfig', () => {
@@ -65,4 +66,42 @@ describe('getConfig', () => {
     const config = getConfig(visData, newVisParams);
     expect(config.yAxes.length).toBe(1);
   });
+
+  it('assigns the correct number of yAxes if the agg is Percentile', () => {
+    const newVisParams = {
+      ...visParamsWithTwoYAxes,
+      seriesParams: [
+        {
+          type: 'line',
+          data: {
+            label: 'Percentiles of bytes',
+            id: '1',
+          },
+          drawLinesBetweenPoints: true,
+          interpolate: 'linear',
+          lineWidth: 2,
+          mode: 'normal',
+          show: true,
+          showCircles: true,
+          circlesRadius: 3,
+          valueAxis: 'ValueAxis-1',
+        },
+      ],
+      dimensions: {
+        ...visParamsWithTwoYAxes.dimensions,
+        y: ['1st', '5th', '25th', '50th', '75th', '95th', '99th'].map((prefix, accessor) => ({
+          label: `${prefix} percentile of bytes`,
+          aggType: 'percentiles',
+          params: {},
+          accessor,
+          format: {
+            id: 'number',
+            params: {},
+          },
+        })),
+      },
+    } as VisParams;
+    const config = getConfig(visDataPercentile, newVisParams);
+    expect(config.yAxes.length).toBe(1);
+  });
 });
diff --git a/src/plugins/vis_types/xy/public/config/get_config.ts b/src/plugins/vis_types/xy/public/config/get_config.ts
index e23fff937ad9bf..d7cf22625e10ed 100644
--- a/src/plugins/vis_types/xy/public/config/get_config.ts
+++ b/src/plugins/vis_types/xy/public/config/get_config.ts
@@ -28,6 +28,7 @@ import { getLegend } from './get_legend';
 import { getAxis } from './get_axis';
 import { getAspects } from './get_aspects';
 import { ChartType } from '../index';
+import { getSafeId } from '../utils/accessors';
 
 export function getConfig(
   table: Datatable,
@@ -51,13 +52,17 @@ export function getConfig(
 
   const yAxes: Array<AxisConfig<ScaleContinuousType>> = [];
 
+  // avoid duplicates based on aggId
+  const aspectVisited = new Set();
   params.dimensions.y.forEach((y) => {
     const accessor = y.accessor;
     const aspect = aspects.y.find(({ column }) => column === accessor);
-    const serie = params.seriesParams.find(({ data: { id } }) => id === aspect?.aggId);
+    const aggId = getSafeId(aspect?.aggId);
+    const serie = params.seriesParams.find(({ data: { id } }) => id === aggId);
     const valueAxis = params.valueAxes.find(({ id }) => id === serie?.valueAxis);
-    if (aspect && valueAxis) {
+    if (aspect && valueAxis && !aspectVisited.has(aggId)) {
       yAxes.push(getAxis<YScaleType>(valueAxis, params.grid, aspect, params.seriesParams));
+      aspectVisited.add(aggId);
     }
   });
 
diff --git a/src/plugins/vis_types/xy/public/mocks.ts b/src/plugins/vis_types/xy/public/mocks.ts
index 6c0de8de1ac368..187850e41b3a8f 100644
--- a/src/plugins/vis_types/xy/public/mocks.ts
+++ b/src/plugins/vis_types/xy/public/mocks.ts
@@ -63,6 +63,86 @@ export const visData = {
   ],
 } as Datatable;
 
+export const visDataPercentile = {
+  type: 'datatable',
+  columns: [
+    {
+      id: 'col-0-1.1',
+      name: '1st percentile of bytes',
+      meta: {
+        type: 'number',
+        field: 'bytes',
+        index: 'kibana_sample_data_logs',
+      },
+    },
+    {
+      id: 'col-1-1.5',
+      name: '5th percentile of bytes',
+      meta: {
+        type: 'number',
+        field: 'bytes',
+        index: 'kibana_sample_data_logs',
+      },
+    },
+    {
+      id: 'col-2-1.25',
+      name: '25th percentile of bytes',
+      meta: {
+        type: 'number',
+        field: 'bytes',
+        index: 'kibana_sample_data_logs',
+      },
+    },
+    {
+      id: 'col-3-1.50',
+      name: '50th percentile of bytes',
+      meta: {
+        type: 'number',
+        field: 'bytes',
+        index: 'kibana_sample_data_logs',
+      },
+    },
+    {
+      id: 'col-4-1.75',
+      name: '75th percentile of bytes',
+      meta: {
+        type: 'number',
+        field: 'bytes',
+        index: 'kibana_sample_data_logs',
+      },
+    },
+    {
+      id: 'col-5-1.95',
+      name: '95th percentile of bytes',
+      meta: {
+        type: 'number',
+        field: 'bytes',
+        index: 'kibana_sample_data_logs',
+      },
+    },
+    {
+      id: 'col-6-1.99',
+      name: '99th percentile of bytes',
+      meta: {
+        type: 'number',
+        field: 'bytes',
+        index: 'kibana_sample_data_logs',
+      },
+    },
+  ],
+  rows: [
+    {
+      'col-0-1.1': 0,
+      'col-1-1.5': 0,
+      'col-2-1.25': 1741.5,
+      'col-3-1.50': 4677,
+      'col-4-1.75': 5681.5,
+      'col-5-1.95': 6816,
+      'col-6-1.99': 6816,
+    },
+  ],
+} as Datatable;
+
 export const visParamsWithTwoYAxes = {
   type: 'histogram',
   addLegend: true,
diff --git a/src/plugins/vis_types/xy/public/utils/accessors.tsx b/src/plugins/vis_types/xy/public/utils/accessors.tsx
index 2b552c9f3f9cf1..6eccb36d6fa732 100644
--- a/src/plugins/vis_types/xy/public/utils/accessors.tsx
+++ b/src/plugins/vis_types/xy/public/utils/accessors.tsx
@@ -79,8 +79,13 @@ export const getSplitSeriesAccessorFnMap = (
 };
 
 // For percentile, the aggregation id is coming in the form %s.%d, where %s is agg_id and %d - percents
-export const isPercentileIdEqualToSeriesId = (columnId: number | string, seriesColumnId: string) =>
-  columnId.toString().split('.')[0] === seriesColumnId;
+export const getSafeId = (columnId?: number | string | null) =>
+  (columnId || '').toString().split('.')[0];
+
+export const isPercentileIdEqualToSeriesId = (
+  columnId: number | string | null | undefined,
+  seriesColumnId: string
+) => getSafeId(columnId) === seriesColumnId;
 
 export const isValidSeriesForDimension = (seriesColumnId: string, { aggId, accessor }: Aspect) =>
   (aggId === seriesColumnId || isPercentileIdEqualToSeriesId(aggId ?? '', seriesColumnId)) &&