[{"settings":{"labourContributions":[{"show":true,"Accrual":true,"_id":"abc","name":"Holidays","amount":10,"target":[{"date":"2021-05-17T23:00:00.000+00:00","percent":4.0},{"date":"2021-05-19T23:00:00.000+00:00","percent":10.0}]},{"show":true,"Accrual":true,"_id":"abd","name":"Taxes","amount":10,"target":[{"date":"2021-04-01T23:00:00.000+00:00","percent":8.0},{"date":"2021-05-27T23:00:00.000+00:00","percent":10.0}]}]}}]

db.collection.aggregate([{$match:{"settings.labourContributions":{$elemMatch:{Accrual:true,target:{$elemMatch:{percent:{$gt:5}}}}}}},{$project:{"settings.labourContributions":{$map:{input:{$filter:{input:"$settings.labourContributions",cond:{$eq:["$$this.Accrual",true]}}},in:{$mergeObjects:["$$this",{target:{$filter:{input:"$$this.target",cond:{$gt:["$$this.percent",5]}}}}]}}}}}])