diff --git a/Sources/XcodeGenKit/PBXProjGenerator.swift b/Sources/XcodeGenKit/PBXProjGenerator.swift
index d169b08f..d21b9c35 100644
--- a/Sources/XcodeGenKit/PBXProjGenerator.swift
+++ b/Sources/XcodeGenKit/PBXProjGenerator.swift
@@ -70,10 +70,17 @@ public class PBXProjGenerator {
         }
 
         let buildConfigs: [XCBuildConfiguration] = spec.configs.map { config in
-            let buildSettings = spec.getProjectBuildSettings(config: config)
+            var buildSettings = spec.getProjectBuildSettings(config: config)
             var baseConfigurationReference: String?
             if let configPath = spec.configFiles[config.name] {
                 baseConfigurationReference = getFileReference(path: basePath + configPath, inPath: basePath)
+                // Do not overwrite xcconfig's value.
+                if let configFile = try? XCConfig(path: basePath + configPath) {
+                    for (k, _) in configFile.flattenedBuildSettings() {
+                        // FIXME: Catch platform specifier. e.g. LD_RUNPATH_SEARCH_PATHS[sdk=iphone*]
+                        buildSettings.removeValue(forKey: k)
+                    }
+                }
             }
             return XCBuildConfiguration(reference: generateUUID(XCBuildConfiguration.self, config.name), name: config.name, baseConfigurationReference: baseConfigurationReference, buildSettings: buildSettings)
         }
@@ -173,6 +180,24 @@ public class PBXProjGenerator {
 
         let configs: [XCBuildConfiguration] = spec.configs.map { config in
             var buildSettings = spec.getTargetBuildSettings(target: target, config: config)
+            // Do not overwrite target's xcconfig values.
+            if let configPath = spec.targets.flatMap({ $0 == target ? $0.configFiles[config.name] : nil }).first {
+                if let configFile = try? XCConfig(path: basePath + configPath) {
+                    for (k, _) in configFile.flattenedBuildSettings() {
+                        // FIXME: Catch platform specifier. e.g. LD_RUNPATH_SEARCH_PATHS[sdk=iphone*]
+                        buildSettings.removeValue(forKey: k)
+                    }
+                }
+            }
+            // Do not overwrite base xcconfig values.
+            if let configPath = spec.configFiles[config.name] {
+                if let configFile = try? XCConfig(path: basePath + configPath) {
+                    for (k, _) in configFile.flattenedBuildSettings() {
+                        // FIXME: Catch platform specifier. e.g. LD_RUNPATH_SEARCH_PATHS[sdk=iphone*]
+                        buildSettings.removeValue(forKey: k)
+                    }
+                }
+            }
 
             // automatically set INFOPLIST_FILE path
             if let plistPath = infoPlists.first,