(Unity Xcode Manipulation API) An example which modifies compiler flags for a given source file.

PbxModifier.cs

using UnityEngine;
using UnityEditor;
using UnityEditor.Callbacks;
using UnityEditor.iOS.Xcode;
using System.IO;

public class PbxModifier
{
    [PostProcessBuild]
    public static void OnPostprocessBuild(BuildTarget buildTarget, string path)
    {
        if (buildTarget == BuildTarget.iOS) {
            string projPath = path + "/Unity-iPhone.xcodeproj/project.pbxproj";

            PBXProject proj = new PBXProject();
            proj.ReadFromString(File.ReadAllText(projPath));

            string target = proj.TargetGuidByName("Unity-iPhone");
            string file = proj.FindFileGuidByProjectPath("Classes/UnityAppController.mm");

            var flags = proj.GetCompileFlagsForFile(target, file);
            flags.Add("-fno-objc-arc");
            proj.SetCompileFlagsForFile(target, file, flags);

            File.WriteAllText(projPath, proj.WriteToString());
        }
    }
}

Where to put this file in Unity Project?

@dilipje In the Editor Folder as a Post Build Script.