diff --git a/build/org.eclipse.cdt.autotools.core/src/org/eclipse/cdt/internal/autotools/core/AutotoolsNewMakeGenerator.java b/build/org.eclipse.cdt.autotools.core/src/org/eclipse/cdt/internal/autotools/core/AutotoolsNewMakeGenerator.java
index 09593196586..1f2687866a1 100644
--- a/build/org.eclipse.cdt.autotools.core/src/org/eclipse/cdt/internal/autotools/core/AutotoolsNewMakeGenerator.java
+++ b/build/org.eclipse.cdt.autotools.core/src/org/eclipse/cdt/internal/autotools/core/AutotoolsNewMakeGenerator.java
@@ -51,6 +51,7 @@ import org.eclipse.cdt.make.core.MakeCorePlugin;
 import org.eclipse.cdt.make.core.makefile.IMakefile;
 import org.eclipse.cdt.make.core.makefile.ITarget;
 import org.eclipse.cdt.make.core.makefile.ITargetRule;
+import org.eclipse.cdt.managedbuilder.buildproperties.IOptionalBuildProperties;
 import org.eclipse.cdt.managedbuilder.core.IBuilder;
 import org.eclipse.cdt.managedbuilder.core.IConfiguration;
 import org.eclipse.cdt.managedbuilder.core.IManagedBuildInfo;
@@ -114,6 +115,9 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 	private static final String TARGET = "buildTarget"; //$NON-NLS-1$
 	private static final String DEFAULT_AUTORECONF = "autoreconf"; //$NON-NLS-1$
 
+	public static final String RUN_IN_CONFIGURE_LAUNCHER = "org.eclipse.cdt.autotools.core.property.launchAutotoolsInContainer"; //$NON-NLS-1$
+
+
 	private IProject project;
 
 	private IProgressMonitor monitor;
@@ -341,6 +345,15 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 		initializeBuildConfigDirs(icfg, toolsCfg);
 
 		ICommandLauncher configureLauncher = CommandLauncherManager.getInstance().getCommandLauncher(project);
+		IOptionalBuildProperties props = icfg.getOptionalBuildProperties();
+		boolean runInCfgLauncher = false;
+		if (props != null) {
+			String runInCfgLauncherProperty = props.getProperty(RUN_IN_CONFIGURE_LAUNCHER);
+			if (runInCfgLauncherProperty != null) {
+				runInCfgLauncher = Boolean.parseBoolean(runInCfgLauncherProperty);
+			}
+		}
+
 
 		// Create the top-level directory for the build output
 		if (!createDirectory(buildDir)) {
@@ -397,7 +410,7 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 						System.arraycopy(newArgs, 0, makeargs, 0, newArgs.length);
 					}
 					makeargs[makeargs.length - 1] = target;
-					rc = runCommand(localCommandLauncher, makeCmd,
+					rc = runCommand(runInCfgLauncher ? configureLauncher : localCommandLauncher, makeCmd,
 							getProjectLocation(),
 							makeargs,
 							AutotoolsPlugin.getResourceString("MakeGenerator.clean.topdir"), //$NON-NLS-1$
@@ -447,7 +460,7 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 								System.arraycopy(newArgs, 0, makeargs, 0, newArgs.length);
 							}
 							makeargs[makeargs.length - 1] = target;
-							rc = runCommand(localCommandLauncher, makeCmd,
+							rc = runCommand(runInCfgLauncher ? configureLauncher : localCommandLauncher, makeCmd,
 									buildLocation,
 									makeargs,
 									AutotoolsPlugin.getFormattedString("MakeGenerator.clean.builddir", new String[]{buildDir}), //$NON-NLS-1$
@@ -509,7 +522,7 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 					configStatus.delete();
 				// Get any user-specified arguments for autogen.
 				String[] autogenArgs = getAutogenArgs(autogenCmdParms);
-				rc = runScript(localCommandLauncher, autogenPath,
+				rc = runScript(runInCfgLauncher ? configureLauncher : localCommandLauncher, autogenPath,
 						autogenPath.removeLastSegments(1), autogenArgs,
 						AutotoolsPlugin.getFormattedString("MakeGenerator.autogen.sh", new String[]{buildDir}), //$NON-NLS-1$
 						errMsg, console, autogenEnvs, consoleStart);
@@ -532,7 +545,7 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 								reconfCmd = DEFAULT_AUTORECONF;
 							IPath reconfCmdPath = new Path(reconfCmd);
 							reconfArgs[0] = "-i"; //$NON-NLS-1$
-							rc = runScript(localCommandLauncher, reconfCmdPath,
+							rc = runScript(runInCfgLauncher ? configureLauncher : localCommandLauncher, reconfCmdPath,
 									getSourcePath(),
 									reconfArgs,
 									AutotoolsPlugin.getFormattedString("MakeGenerator.autoreconf", new String[]{buildDir}), //$NON-NLS-1$
@@ -565,7 +578,7 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 				String[] makeargs = new String[1];
 				IPath makeCmd = builder.getBuildCommand();
 				makeargs[0] = "-f" + getMakefileCVSPath().toOSString(); //$NON-NLS-1$
-				rc = runCommand(localCommandLauncher, makeCmd,
+				rc = runCommand(runInCfgLauncher ? configureLauncher : localCommandLauncher, makeCmd,
 						getProjectLocation().append(buildDir),
 						makeargs,
 						AutotoolsPlugin.getFormattedString("MakeGenerator.makefile.cvs", new String[]{buildDir}), //$NON-NLS-1$
@@ -597,7 +610,7 @@ public class AutotoolsNewMakeGenerator extends MarkerGenerator {
 					reconfCmd = DEFAULT_AUTORECONF;
 				IPath reconfCmdPath = new Path(reconfCmd);
 				reconfArgs[0] = "-i"; //$NON-NLS-1$
-				rc = runScript(localCommandLauncher, reconfCmdPath,
+				rc = runScript(runInCfgLauncher ? configureLauncher : localCommandLauncher, reconfCmdPath,
 						getSourcePath(),
 						reconfArgs,
 						AutotoolsPlugin.getFormattedString("MakeGenerator.autoreconf", new String[]{buildDir}), //$NON-NLS-1$
diff --git a/build/org.eclipse.cdt.autotools.ui/src/org/eclipse/cdt/internal/autotools/ui/actions/AbstractAutotoolsHandler.java b/build/org.eclipse.cdt.autotools.ui/src/org/eclipse/cdt/internal/autotools/ui/actions/AbstractAutotoolsHandler.java
index d26e6cc9643..ae18900b0e8 100644
--- a/build/org.eclipse.cdt.autotools.ui/src/org/eclipse/cdt/internal/autotools/ui/actions/AbstractAutotoolsHandler.java
+++ b/build/org.eclipse.cdt.autotools.ui/src/org/eclipse/cdt/internal/autotools/ui/actions/AbstractAutotoolsHandler.java
@@ -20,6 +20,7 @@ import java.util.StringTokenizer;
 import org.eclipse.cdt.autotools.ui.AutotoolsUIPlugin;
 import org.eclipse.cdt.core.CCorePlugin;
 import org.eclipse.cdt.core.CommandLauncher;
+import org.eclipse.cdt.core.CommandLauncherManager;
 import org.eclipse.cdt.core.ConsoleOutputStream;
 import org.eclipse.cdt.core.ICommandLauncher;
 import org.eclipse.cdt.core.envvar.IEnvironmentVariable;
@@ -28,6 +29,7 @@ import org.eclipse.cdt.core.model.ICElement;
 import org.eclipse.cdt.core.model.ICProject;
 import org.eclipse.cdt.core.resources.IConsole;
 import org.eclipse.cdt.internal.autotools.core.AutotoolsNewMakeGenerator;
+import org.eclipse.cdt.managedbuilder.buildproperties.IOptionalBuildProperties;
 import org.eclipse.cdt.managedbuilder.core.IConfiguration;
 import org.eclipse.cdt.managedbuilder.core.IManagedBuildInfo;
 import org.eclipse.cdt.managedbuilder.core.ManagedBuildManager;
@@ -300,9 +302,23 @@ public abstract class AbstractAutotoolsHandler extends AbstractHandler {
 
 						ArrayList<String> additionalEnvs = new ArrayList<>();
 						String strippedCommand = AutotoolsNewMakeGenerator.stripEnvVars(command, additionalEnvs);
-						// Get a launcher for the config command...default non-remote to use local
-						// commands
-						RemoteCommandLauncher launcher = new RemoteCommandLauncher(new CommandLauncher());
+						// Get a launcher for the config command...default for non-remote is a local
+						// launcher, but user can override to perform all Autotool commands in a
+						// Container when build in Container is enabled so check optional build
+						// properties
+						IOptionalBuildProperties props = cfg.getOptionalBuildProperties();
+						boolean runInContainer = false;
+						if (props != null) {
+							String runInContainerProperty = props
+									.getProperty(AutotoolsNewMakeGenerator.RUN_IN_CONFIGURE_LAUNCHER);
+							if (runInContainerProperty != null) {
+								runInContainer = Boolean.parseBoolean(runInContainerProperty);
+							}
+						}
+						ICommandLauncher fallbackLauncher = runInContainer
+								? CommandLauncherManager.getInstance().getCommandLauncher(project)
+								: new CommandLauncher();
+						RemoteCommandLauncher launcher = new RemoteCommandLauncher(fallbackLauncher);
 						launcher.setProject(project);
 						// Set the environment
 						IEnvironmentVariable variables[] = ManagedBuildManager.getEnvironmentVariableProvider()
diff --git a/launch/org.eclipse.cdt.docker.launcher/src/org/eclipse/cdt/internal/docker/launcher/ContainerPropertyTab.java b/launch/org.eclipse.cdt.docker.launcher/src/org/eclipse/cdt/internal/docker/launcher/ContainerPropertyTab.java
index 623a4c5acea..92d11aeb678 100644
--- a/launch/org.eclipse.cdt.docker.launcher/src/org/eclipse/cdt/internal/docker/launcher/ContainerPropertyTab.java
+++ b/launch/org.eclipse.cdt.docker.launcher/src/org/eclipse/cdt/internal/docker/launcher/ContainerPropertyTab.java
@@ -28,6 +28,7 @@ import org.eclipse.cdt.core.settings.model.ICMultiConfigDescription;
 import org.eclipse.cdt.core.settings.model.ICResourceDescription;
 import org.eclipse.cdt.core.settings.model.ICTargetPlatformSetting;
 import org.eclipse.cdt.docker.launcher.ContainerCommandLauncher;
+import org.eclipse.cdt.docker.launcher.DockerLaunchUIPlugin;
 import org.eclipse.cdt.internal.docker.launcher.ContainerPropertyVolumesModel.MountType;
 import org.eclipse.cdt.managedbuilder.buildproperties.IOptionalBuildProperties;
 import org.eclipse.cdt.managedbuilder.core.IConfiguration;
@@ -42,6 +43,9 @@ import org.eclipse.core.databinding.beans.IBeanValueProperty;
 import org.eclipse.core.databinding.observable.list.IObservableList;
 import org.eclipse.core.databinding.observable.map.IObservableMap;
 import org.eclipse.core.databinding.property.Properties;
+import org.eclipse.core.resources.IProject;
+import org.eclipse.core.resources.IProjectNature;
+import org.eclipse.core.runtime.CoreException;
 import org.eclipse.jface.databinding.viewers.ObservableListContentProvider;
 import org.eclipse.jface.databinding.viewers.ObservableMapLabelProvider;
 import org.eclipse.jface.databinding.viewers.ViewerSupport;
@@ -88,19 +92,23 @@ public class ContainerPropertyTab extends AbstractCBuildPropertyTab
 
 	private final static String GNU_ELF_PARSER_ID = "org.eclipse.cdt.core.GNU_ELF"; //$NON-NLS-1$
 	private final static String ELF_PARSER_ID = "org.eclipse.cdt.core.ELF"; //$NON-NLS-1$
+	private static final String RUN_IN_CONFIGURE_LAUNCHER = "org.eclipse.cdt.autotools.core.property.launchAutotoolsInContainer"; //$NON-NLS-1$
 
 	private Combo imageCombo;
 	private Combo connectionSelector;
 	private Button enableButton;
+	private Button launchAutotoolsButton;
 	private Button addButton;
 	private IDockerConnection connection;
 	private IDockerConnection[] connections;
 	private IDockerImageListener containerTab;
+	private boolean isAutotoolsProject;
 
 	private String connectionName;
 	private String connectionUri = ""; //$NON-NLS-1$
 
 	private boolean initialEnabled;
+	private boolean initialAutotoolsLaunchEnabled;
 	private String initialConnection;
 	private String initialImageId;
 	private String initialVolumes;
@@ -235,6 +243,43 @@ public class ContainerPropertyTab extends AbstractCBuildPropertyTab
 
 		});
 
+		createVolumeSettingsContainer(usercomp);
+
+		try {
+			IProject project = iCfgd.getProjectDescription().getProject();
+			IProjectNature nature = project.getNature(
+					"org.eclipse.cdt.autotools.core.autotoolsNatureV2"); //$NON-NLS-1$
+			isAutotoolsProject = (nature != null);
+			if (isAutotoolsProject) {
+				launchAutotoolsButton = new Button(usercomp, SWT.CHECK);
+				launchAutotoolsButton.setText(
+						Messages.ContainerPropertyTab_Run_Autotools_In_Container_Msg);
+				launchAutotoolsButton.setToolTipText(
+						Messages.ContainerPropertyTab_Run_Autotools_In_Container_Tooltip);
+				gd = new GridData(GridData.FILL_HORIZONTAL);
+				gd.horizontalSpan = 5;
+				launchAutotoolsButton.setLayoutData(gd);
+				initializeLaunchAutotoolsButton();
+				launchAutotoolsButton
+						.addSelectionListener(new SelectionListener() {
+
+							@Override
+							public void widgetSelected(SelectionEvent e) {
+								setLaunchAutotoolsEnablement(
+										launchAutotoolsButton.getSelection());
+							}
+
+							@Override
+							public void widgetDefaultSelected(
+									SelectionEvent e) {
+								// ignore
+							}
+						});
+			}
+		} catch (CoreException e) {
+			DockerLaunchUIPlugin.log(e);
+		}
+
 		initializeEnablementButton();
 		enableButton.addSelectionListener(new SelectionListener() {
 
@@ -251,7 +296,6 @@ public class ContainerPropertyTab extends AbstractCBuildPropertyTab
 
 		});
 
-		createVolumeSettingsContainer(usercomp);
 	}
 
 	private void createVolumeSettingsContainer(final Composite container) {
@@ -597,6 +641,23 @@ public class ContainerPropertyTab extends AbstractCBuildPropertyTab
 		}
 	}
 
+	private void setLaunchAutotoolsEnablement(boolean enabled) {
+		if (iCfg instanceof IMultiConfiguration) {
+			IConfiguration[] cfs = (IConfiguration[]) ((IMultiConfiguration) iCfg)
+					.getItems();
+			for (int i = 0; i < cfs.length; i++) {
+				IConfiguration cfg = cfs[i];
+				IOptionalBuildProperties p = cfg.getOptionalBuildProperties();
+				p.setProperty(RUN_IN_CONFIGURE_LAUNCHER,
+						Boolean.toString(launchAutotoolsButton.getSelection()));
+			}
+		} else {
+			IOptionalBuildProperties p = iCfg.getOptionalBuildProperties();
+			p.setProperty(RUN_IN_CONFIGURE_LAUNCHER,
+					Boolean.toString(launchAutotoolsButton.getSelection()));
+		}
+	}
+
 	private void setImageId(String imageId) {
 		if (iCfg instanceof IMultiConfiguration) {
 			IConfiguration[] cfs = (IConfiguration[]) ((IMultiConfiguration) iCfg)
@@ -630,6 +691,9 @@ public class ContainerPropertyTab extends AbstractCBuildPropertyTab
 	private void setControlsEnabled(boolean enabled) {
 		imageCombo.setEnabled(enabled);
 		connectionSelector.setEnabled(enabled);
+		if (isAutotoolsProject) {
+			launchAutotoolsButton.setEnabled(enabled);
+		}
 		setVolumeControlsEnabled(new Button[] { addButton }, enabled);
 	}
 
@@ -646,6 +710,16 @@ public class ContainerPropertyTab extends AbstractCBuildPropertyTab
 		setControlsEnabled(initialEnabled);
 	}
 
+	private void initializeLaunchAutotoolsButton() {
+		initialEnabled = false;
+		IOptionalBuildProperties properties = iCfg.getOptionalBuildProperties();
+		String savedEnabled = properties.getProperty(RUN_IN_CONFIGURE_LAUNCHER);
+		if (savedEnabled != null) {
+			initialAutotoolsLaunchEnabled = Boolean.parseBoolean(savedEnabled);
+		}
+		launchAutotoolsButton.setSelection(initialAutotoolsLaunchEnabled);
+	}
+
 	private void initializeConnectionSelector() {
 		int defaultIndex = -1;
 		initialConnection = null;
@@ -871,6 +945,8 @@ public class ContainerPropertyTab extends AbstractCBuildPropertyTab
 				.getProperty(ContainerCommandLauncher.VOLUMES_ID);
 		initialSelectedVolumes = properties
 				.getProperty(ContainerCommandLauncher.SELECTED_VOLUMES_ID);
+		initialAutotoolsLaunchEnabled = Boolean.parseBoolean(
+				properties.getProperty(RUN_IN_CONFIGURE_LAUNCHER));
 		List<ILanguageSettingsProvider> providers = ((ILanguageSettingsProvidersKeeper) cfgd)
 				.getLanguageSettingProviders();
 		for (ILanguageSettingsProvider provider : providers) {
diff --git a/launch/org.eclipse.cdt.docker.launcher/src/org/eclipse/cdt/internal/docker/launcher/Messages.java b/launch/org.eclipse.cdt.docker.launcher/src/org/eclipse/cdt/internal/docker/launcher/Messages.java
index dc90a4e3144..ac7ec788d2e 100644
--- a/launch/org.eclipse.cdt.docker.launcher/src/org/eclipse/cdt/internal/docker/launcher/Messages.java
+++ b/launch/org.eclipse.cdt.docker.launcher/src/org/eclipse/cdt/internal/docker/launcher/Messages.java
@@ -99,6 +99,8 @@ public class Messages extends NLS {
 
 	public static String ContainerPropertyTab_Title;
 	public static String ContainerPropertyTab_Enable_Msg;
+	public static String ContainerPropertyTab_Run_Autotools_In_Container_Msg;
+	public static String ContainerPropertyTab_Run_Autotools_In_Container_Tooltip;
 
 	public static String ContainerCommandLauncher_image_msg;
 	public static String CommandLauncher_CommandCancelled;
diff --git a/launch/org.eclipse.cdt.docker.launcher/src/org/eclipse/cdt/internal/docker/launcher/messages.properties b/launch/org.eclipse.cdt.docker.launcher/src/org/eclipse/cdt/internal/docker/launcher/messages.properties
index 06609d611cf..a545210b63a 100644
--- a/launch/org.eclipse.cdt.docker.launcher/src/org/eclipse/cdt/internal/docker/launcher/messages.properties
+++ b/launch/org.eclipse.cdt.docker.launcher/src/org/eclipse/cdt/internal/docker/launcher/messages.properties
@@ -42,6 +42,8 @@ ContainerTab_Warning_Image_Not_Found=Docker Image: {0} is not a valid pulled ima
 
 ContainerPropertyTab_Title=Container Settings
 ContainerPropertyTab_Enable_Msg=Build inside Docker Image
+ContainerPropertyTab_Run_Autotools_In_Container_Msg=Run all Autotools in Container
+ContainerPropertyTab_Run_Autotools_In_Container_Tooltip=Run Autotool commands in the Docker Container.  This may cause inconsistencies between configurations sharing generated files.
 
 HeaderPreferencePage_Connection_Label=Connection
 HeaderPreferencePage_Image_Label=Image