Hi Raj Vakati ,
I moved the query out from the loop, still I am getting the System.LimitException: Too many SOQL queries: 101.  through the process builder:

trigger LeadIntegrationTrigger on Lead (after update, after insert)
{
    
    List<String> LeadNames = new List<String>{};
    Set<ID> Oppid =new Set<ID>();
    List<Contact>lcon = New List<Contact>();
    List<OpportunityLineItem> ListLine = New List<OpportunityLineItem>();
    List<Opportunity> OppList = New List<Opportunity>();
    
    //After Save and status = Qualifield will auto convert
    if (Trigger.isInsert) {
        for(Lead aLead: Trigger.new){
            //try{
                if((aLead.isconverted==false) && (aLead.Status == 'Qualified - Enrolled')) {
                    Database.LeadConvert lc = new database.LeadConvert();
                    lc.setLeadId(aLead.Id);
                    lc.convertedStatus = 'Qualified - Enrolled';
                    lc.setDoNotCreateOpportunity(false);
                    Database.LeadConvertResult lcr = Database.convertLead(lc);
                    System.assert(lcr.isSuccess());
                    //aLead.IsConverted=false;
                }
            //}
            // Validate If Phone Lead wrong
            //catch(System.DmlException ee){
              //  aLead.addError('Phone number must contains 10 digit and start with 0 Or Gender is not input');
            //}        
        }
    
    }
    
    if (Trigger.isUpdate ) {
        List<OpportunityStudent__c> aNewStudents = new List<OpportunityStudent__c>();
        Map<Id, Lead> aLeadToCheck = new Map<Id, Lead>();
        Map<Id, Lead> aContactToCheck = new Map<Id, Lead>();
        
        for(Integer x = 0; x < Trigger.new.size(); x++)
            {        
                    if((Trigger.new[x].isconverted==false) && (Trigger.new[x].Status == 'Qualified - Enrolled'&&Trigger.new[x].Status!=Trigger.old[x].Status)) {
                    Database.LeadConvert lc = new database.LeadConvert();
                    lc.setLeadId(Trigger.new[x].Id);
                    lc.convertedStatus = 'Qualified - Enrolled';
                    lc.setDoNotCreateOpportunity(false);
                    Database.LeadConvertResult lcr = Database.convertLead(lc);
                    System.assert(lcr.isSuccess());
                   }
        
        
            if (Trigger.new[x].IsConverted == true && Trigger.oldMap.get(Trigger.new[x].Id).IsConverted == false&& Trigger.new[x].ConvertedOpportunityId != null && Trigger.new[x].ConvertedContactId != null){  
                aLeadToCheck.put(Trigger.new[x].ConvertedOpportunityId, Trigger.new[x]);
                aContactToCheck.put(Trigger.new[x].ConvertedContactId, Trigger.new[x]);
            }
        }
         
        //Auto add student on Opportuntiy
        List<Opportunity> anOppList = [SELECT Id, AccountId, Account.Name,account.recordtype.name FROM Opportunity WHERE Id IN :aLeadToCheck.keySet()];
        List<Contact> acontactList = [SELECT Id,Avetmiss_At_School__c,Contact_Method__c,Avetmiss_Country_Of_Birth__c,
                Avetmiss_Disability__c,Avetmiss_Disability_List__c,Gender__c,Avetmiss_Highest_School_Level__c,
                Avetmiss_Indigenous_Status__c,Avetmiss_Labour_Force_Status__c,Avetmiss_Learner_Unique_Identifier__c,
                Avetmiss_Main_Language__c,Avetmiss_Nationality__c,Avetmiss_Prior_Education__c,Prior_Education__c,Avetmiss_Prior_Education_List__c,
                Avetmiss_School_Identifier__c,Avetmiss_Spoken_English_Proefficiency__c,Avetmiss_Year_Highest_School_Level__c,BirthDate
                FROM Contact  WHERE Id IN :aContactToCheck.keySet()];
        
        
       for(Contact aCon:acontactList) {
             if (aCon.Id != NULL){
                   Lead myLead = aContactToCheck.get(aCon.Id);
             
                aCon.Avetmiss_At_School__c=myLead.Avetmiss_At_School__c;
                aCon.Birthdate=myLead.Birthdate__c;
                // Making Mandatory 'Email' as the Contact Method
                aCon.Contact_Method__c= 'Email';
                aCon.Avetmiss_Country_Of_Birth__c=myLead.Avetmiss_Country_Of_Birth__c;
                aCon.Avetmiss_Disability__c=myLead.Avetmiss_Disability__c;
                aCon.Avetmiss_Disability_List__c=myLead.Avetmiss_Disability_List__c;
                aCon.Gender__c=myLead.Gender__c;
                aCon.Avetmiss_Highest_School_Level__c=myLead.Avetmiss_Highest_School_Level__c;
                aCon.Avetmiss_Indigenous_Status__c = myLead.Avetmiss_Indigenous_Status__c;
                aCon.Avetmiss_Labour_Force_Status__c= myLead.Avetmiss_Labour_Force_Status__c;
                aCon.Avetmiss_Learner_Unique_Identifier__c = myLead.Avetmiss_Learner_Unique_Identifier__c;
                aCon.Avetmiss_Main_Language__c = myLead.Avetmiss_Main_Language__c;
                aCon.Avetmiss_Nationality__c = myLead.Avetmiss_Nationality__c;
                aCon.Avetmiss_Prior_Education__c = myLead.Avetmiss_Prior_Education__c;
                aCon.Town_of_Birth__c = myLead.Town_of_Birth__c;
                aCon.State_of_Birth__c = myLead.State_of_Birth__c;
                aCon.MobilePhone = myLead.MobilePhone;
                aCon.Email = myLead.Email;
                aCon.Login__c = myLead.Email;
                aCon.Prior_Education__c = myLead.Prior_Education__c;
                aCon.Disability__c= myLead.Disability__c;
                aCon.Avetmiss_Prior_Education_List__c = myLead.Avetmiss_Prior_Education_List__c;
                aCon.Avetmiss_School_Identifier__c = myLead.Avetmiss_School_Identifier__c;
                aCon.Avetmiss_Spoken_English_Proefficiency__c = myLead.Avetmiss_Spoken_English_Proefficiency__c;
                aCon.Avetmiss_Year_Highest_School_Level__c = myLead.Avetmiss_Year_Highest_School_Level__c;
                }
           lcon.add(aCon);
       }
        
        
        
        
        
        
        
        
        
        for (Opportunity anOpp: anOppList){
        
           if (anOpp.AccountId != null){
                Lead aLead = aLeadToCheck.get(anOpp.Id);
                //update Opportunity Detail
                anOpp.Course_Amount__c=aLead.Course_Amount__c;
                anOpp.Course_Start_Date__c=aLead.Course_Start_Date__c;
                anOpp.Course_End_Date__c=aLead.Course_End_Date__c;
                anOpp.Training_Program__c=aLead.Product__c;
                OppList.add(anOpp);
               
               /*
                //
                Contact con=[SELECT id,Avetmiss_At_School__c,Contact_Method__c,Avetmiss_Country_Of_Birth__c,
                Avetmiss_Disability__c,Avetmiss_Disability_List__c,Gender__c,Avetmiss_Highest_School_Level__c,
                Avetmiss_Indigenous_Status__c,Avetmiss_Labour_Force_Status__c,Avetmiss_Learner_Unique_Identifier__c,
                Avetmiss_Main_Language__c,Avetmiss_Nationality__c,Avetmiss_Prior_Education__c,Prior_Education__c,Avetmiss_Prior_Education_List__c,
                Avetmiss_School_Identifier__c,Avetmiss_Spoken_English_Proefficiency__c,Avetmiss_Year_Highest_School_Level__c,BirthDate
                FROM contact WHERE id=:aLead.ConvertedContactId];
                system.debug('Cloning');
                //Clone data to personAccount
                con.Avetmiss_At_School__c=aLead.Avetmiss_At_School__c;
                con.Birthdate=aLead.Birthdate__c;
                // Making Mandatory 'Email' as the Contact Method
                con.Contact_Method__c= 'Email';
                con.Avetmiss_Country_Of_Birth__c=aLead.Avetmiss_Country_Of_Birth__c;
                con.Avetmiss_Disability__c=aLead.Avetmiss_Disability__c;
                con.Avetmiss_Disability_List__c=aLead.Avetmiss_Disability_List__c;
                con.Gender__c=aLead.Gender__c;
                con.Avetmiss_Highest_School_Level__c=aLead.Avetmiss_Highest_School_Level__c;
                con.Avetmiss_Indigenous_Status__c = aLead.Avetmiss_Indigenous_Status__c;
                con.Avetmiss_Labour_Force_Status__c= aLead.Avetmiss_Labour_Force_Status__c;
                con.Avetmiss_Learner_Unique_Identifier__c = aLead.Avetmiss_Learner_Unique_Identifier__c;
                con.Avetmiss_Main_Language__c = aLead.Avetmiss_Main_Language__c;
                con.Avetmiss_Nationality__c = aLead.Avetmiss_Nationality__c;
                con.Avetmiss_Prior_Education__c = aLead.Avetmiss_Prior_Education__c;
                con.Town_of_Birth__c = aLead.Town_of_Birth__c;
                con.State_of_Birth__c = aLead.State_of_Birth__c;
                               
                con.MobilePhone = aLead.MobilePhone;
                con.Email = aLead.Email;
                con.Login__c = aLead.Email;
                con.Prior_Education__c = aLead.Prior_Education__c;
                con.Disability__c= aLead.Disability__c;
                con.Avetmiss_Prior_Education_List__c = aLead.Avetmiss_Prior_Education_List__c;
                con.Avetmiss_School_Identifier__c = aLead.Avetmiss_School_Identifier__c;
                con.Avetmiss_Spoken_English_Proefficiency__c = aLead.Avetmiss_Spoken_English_Proefficiency__c;
                con.Avetmiss_Year_Highest_School_Level__c = aLead.Avetmiss_Year_Highest_School_Level__c;
                lcon.add(con);
                // end clone data
                
                */
                
                //Add New PricebookEntry
                if(aLead.Product__c!=null){
                    PricebookEntry Pricebook=[SELECT id FROM PricebookEntry WHERE Product2Id=:aLead.Product__c Limit 1];
                    /*PricebookEntry Pricebook = new PricebookEntry();
                    Pricebook.Pricebook2Id=Pbook.id;
                    Pricebook.Product2Id=aLead.Product__c;
                    Pricebook.UseStandardPrice=true;
                    insert Pricebook;
                    */
                    //
                    //Add Product Line
                    /*
                    OpportunityLineItem OppLi = new OpportunityLineItem();
                    OppLi.OpportunityId=anOpp.id;
                   
                    OppLi.PricebookEntryId=Pricebook.id;
                    OppLi.Quantity=1;
                    OppLi.UnitPrice=1000;
                    
                    ListLine.add(OppLi);
                    */
                }                    
                OpportunityStudent__c aNewStudent = new OpportunityStudent__c();
                aNewStudent.Contact__c = aLead.ConvertedContactId;
                aNewStudent.Opportunity__c = aLead.ConvertedOpportunityId;                                          
                Oppid.add(aNewStudent.Opportunity__c);
                aNewStudents.add(aNewStudent);
                system.debug('@@@@@ CCCC');
            }
            else{
                Oppid.add(anOpp.id);
            }
        }
        
        //Prevent Duplicate Manage student [Person Acccount]
        try{
            List <OpportunityContactRole> Role=[SELECT id,opportunityid FROM OpportunityContactRole WHERE Opportunityid in : Oppid];
            delete Role;
        }
        catch(System.QueryException e){}
        
        insert aNewStudents;
        //insert ListLine;
        update OppList;
        update lcon;   
        List<OpportunityStudent__c> ListStudent=[SELECT id,Opportunity__c,Contact__c FROM OpportunityStudent__c WHERE Opportunity__c in:Oppid];
        IF(ListStudent.size()>1){
            delete ListStudent[1];
        }    
    }
}