diff --git a/main/command/src/main/scala/sbt/State.scala b/main/command/src/main/scala/sbt/State.scala
index bc79ba7a7..64cdf80e7 100644
--- a/main/command/src/main/scala/sbt/State.scala
+++ b/main/command/src/main/scala/sbt/State.scala
@@ -178,16 +178,16 @@ object State {
   /** Provides operations and transformations on State. */
   implicit def stateOps(s: State): StateOps = new StateOps {
     def process(f: (String, State) => State): State = {
-      def doX(x: String, xs: Seq[String]) = {
-        log.debug(s"> $x")
-        f(x, s.copy(remainingCommands = xs, history = x :: s.history))
+      def runCmd(cmd: String, remainingCommands: Seq[String]) = {
+        log.debug(s"> $cmd")
+        f(cmd, s.copy(remainingCommands = remainingCommands, history = cmd :: s.history))
       }
-      def isInteractive = System.console() != null
-      def hasInput = System.console().reader().ready()
+      def isInteractive = System.console != null
+      def hasInput = Option(System.console) exists (_.reader.ready())
       def hasShellCmd = s.definedCommands exists { case c: SimpleCommand => c.name == Shell; case _ => false }
       s.remainingCommands match {
-        case Seq()           => if (isInteractive && hasInput && hasShellCmd) doX(Shell, Nil) else exit(true)
-        case Seq(x, xs @ _*) => doX(x, xs)
+        case Seq()           => if (isInteractive && hasInput && hasShellCmd) runCmd(Shell, Nil) else exit(true)
+        case Seq(x, xs @ _*) => runCmd(x, xs)
       }
     }
     def :::(newCommands: Seq[String]): State = s.copy(remainingCommands = newCommands ++ s.remainingCommands)
diff --git a/main/src/main/scala/sbt/Keys.scala b/main/src/main/scala/sbt/Keys.scala
index fd75b43ba..439896c12 100644
--- a/main/src/main/scala/sbt/Keys.scala
+++ b/main/src/main/scala/sbt/Keys.scala
@@ -64,6 +64,7 @@ object Keys {
   val shellPrompt = SettingKey(BasicKeys.shellPrompt)
   val analysis = AttributeKey[inc.Analysis]("analysis", "Analysis of compilation, including dependencies and generated outputs.", DSetting)
   val watch = SettingKey(BasicKeys.watch)
+  val suppressSbtShellNotification = SettingKey[Boolean]("suppressSbtShellNotification", """True to suppress the "Executing in batch mode.." message.""", CSetting)
   val pollInterval = SettingKey[Int]("poll-interval", "Interval between checks for modified sources by the continuous execution command.", BMinusSetting)
   val watchSources = TaskKey[Seq[File]]("watch-sources", "Defines the sources in this project for continuous execution to watch for changes.", BMinusSetting)
   val watchTransitiveSources = TaskKey[Seq[File]]("watch-transitive-sources", "Defines the sources in all projects for continuous execution to watch.", CSetting)
diff --git a/main/src/main/scala/sbt/Main.scala b/main/src/main/scala/sbt/Main.scala
index 5bd13fd6a..cffeb90d1 100644
--- a/main/src/main/scala/sbt/Main.scala
+++ b/main/src/main/scala/sbt/Main.scala
@@ -18,7 +18,7 @@ import java.net.URI
 import java.util.Locale
 import scala.util.control.NonFatal
 
-import BasicCommandStrings.Shell
+import BasicCommandStrings.{ Shell, TemplateCommand }
 import CommandStrings.BootCommand
 
 /** This class is the entry point for sbt. */
@@ -29,59 +29,11 @@ final class xMain extends xsbti.AppMain {
       import BasicCommandStrings.runEarly
       import BuiltinCommands.{ initialize, defaults }
       import CommandStrings.{ BootCommand, DefaultsCommand, InitCommand }
-      if (!java.lang.Boolean.getBoolean("sbt.skip.version.write"))
-        setSbtVersion(configuration.baseDirectory(), configuration.provider().id().version())
       val state = initialState(configuration,
         Seq(defaults, early),
         runEarly(DefaultsCommand) :: runEarly(InitCommand) :: BootCommand :: Nil)
-      notifyUsersAboutShell(state)
       runManaged(state)
     }
-
-  private val sbtVersionRegex = """sbt\.version\s*=.*""".r
-  private def isSbtVersionLine(s: String) = sbtVersionRegex.pattern matcher s matches ()
-
-  private def isSbtProject(baseDir: File, projectDir: File) =
-    projectDir.exists() || (baseDir * "*.sbt").get.nonEmpty
-
-  private def setSbtVersion(baseDir: File, sbtVersion: String) = {
-    val projectDir = baseDir / "project"
-    val buildProps = projectDir / "build.properties"
-
-    val buildPropsLines = if (buildProps.canRead) IO.readLines(buildProps) else Nil
-
-    val sbtVersionAbsent = buildPropsLines forall (!isSbtVersionLine(_))
-
-    if (sbtVersionAbsent) {
-      val errorMessage = s"WARN: No sbt.version set in project/build.properties, base directory: $baseDir"
-      try {
-        if (isSbtProject(baseDir, projectDir)) {
-          val line = s"sbt.version=$sbtVersion"
-          IO.writeLines(buildProps, line :: buildPropsLines)
-          println(s"Updated file $buildProps setting sbt.version to: $sbtVersion")
-        } else
-          println(errorMessage)
-      } catch {
-        case _: IOException => println(errorMessage)
-      }
-    }
-  }
-
-  private def isInteractive = System.console() != null
-  private def hasShell(state: State) = state.remainingCommands contains Shell
-
-  /**
-   * The "boot" command adds "iflast shell" ("if last shell")
-   * which basically means it falls back to shell if there are no further commands
-   */
-  private def endsWithBoot(state: State) = state.remainingCommands.lastOption exists (_ == BootCommand)
-
-  private def notifyUsersAboutShell(state: State) =
-    if (isInteractive && !hasShell(state) && !endsWithBoot(state)) {
-      state.log warn "Executing in batch mode."
-      state.log warn "  For better performance, hit [ENTER] to switch to interactive mode, or"
-      state.log warn "  consider launching sbt without any commands, or explicitly passing 'shell'"
-    }
 }
 
 final class ScriptMain extends xsbti.AppMain {
@@ -143,9 +95,11 @@ object BuiltinCommands {
     projects, project, reboot, read, history, set, sessionCommand, inspect, loadProjectImpl, loadFailed,
     Cross.crossBuild, Cross.switchVersion, PluginCross.pluginCross, PluginCross.pluginSwitch,
     setOnFailure, clearOnFailure, stashOnFailure, popOnFailure, setLogLevel, plugin, plugins,
+    writeSbtVersion, notifyUsersAboutShell,
     ifLast, multi, shell, continuous, eval, alias, append, last, lastGrep, export, boot, nop, call, exit, early, initialize, act) ++
     compatCommands
-  def DefaultBootCommands: Seq[String] = LoadProject :: (IfLast + " " + Shell) :: Nil
+  def DefaultBootCommands: Seq[String] =
+    WriteSbtVersion :: LoadProject :: NotifyUsersAboutShell :: s"$IfLast $Shell" :: Nil
 
   def boot = Command.make(BootCommand)(bootParser)
 
@@ -573,4 +527,61 @@ object BuiltinCommands {
         }
       s.put(Keys.stateCompilerCache, cache)
     }
+
+  private val sbtVersionRegex = """sbt\.version\s*=.*""".r
+  private def isSbtVersionLine(s: String) = sbtVersionRegex.pattern matcher s matches ()
+
+  private def isSbtProject(baseDir: File, projectDir: File) =
+    projectDir.exists() || (baseDir * "*.sbt").get.nonEmpty
+
+  private def writeSbtVersionUnconditionally(state: State) = {
+    val baseDir = state.baseDir
+    val sbtVersion = BuiltinCommands.sbtVersion(state)
+    val projectDir = baseDir / "project"
+    val buildProps = projectDir / "build.properties"
+
+    val buildPropsLines = if (buildProps.canRead) IO.readLines(buildProps) else Nil
+
+    val sbtVersionAbsent = buildPropsLines forall (!isSbtVersionLine(_))
+
+    if (sbtVersionAbsent) {
+      val warnMsg = s"No sbt.version set in project/build.properties, base directory: $baseDir"
+      try {
+        if (isSbtProject(baseDir, projectDir)) {
+          val line = s"sbt.version=$sbtVersion"
+          IO.writeLines(buildProps, line :: buildPropsLines)
+          state.log info s"Updated file $buildProps: set sbt.version to $sbtVersion"
+        } else
+          state.log warn warnMsg
+      } catch {
+        case _: IOException => state.log warn warnMsg
+      }
+    }
+  }
+
+  private def intendsToInvokeNew(state: State) = state.remainingCommands contains TemplateCommand
+
+  private def writeSbtVersion(state: State) =
+    if (!java.lang.Boolean.getBoolean("sbt.skip.version.write") && !intendsToInvokeNew(state))
+      writeSbtVersionUnconditionally(state)
+
+  private def WriteSbtVersion = "write-sbt-version"
+
+  private def writeSbtVersion: Command =
+    Command.command(WriteSbtVersion) { state => writeSbtVersion(state); state }
+
+  private def isInteractive = System.console() != null
+
+  private def intendsToInvokeCompile(state: State) = state.remainingCommands contains Keys.compile.key.label
+
+  private def notifyUsersAboutShell(state: State): Unit = {
+    val suppress = Project extract state getOpt Keys.suppressSbtShellNotification getOrElse false
+    if (!suppress && isInteractive && intendsToInvokeCompile(state))
+      state.log info "Executing in batch mode. For better performance use sbt's shell; hit [ENTER] to do so now"
+  }
+
+  private def NotifyUsersAboutShell = "notify-users-about-shell"
+
+  private def notifyUsersAboutShell: Command =
+    Command.command(NotifyUsersAboutShell) { state => notifyUsersAboutShell(state); state }
 }
diff --git a/notes/0.13.16/tweak-new-startup-messages.markdown b/notes/0.13.16/tweak-new-startup-messages.markdown
new file mode 100644
index 000000000..756826049
--- /dev/null
+++ b/notes/0.13.16/tweak-new-startup-messages.markdown
@@ -0,0 +1,36 @@
+### Improvements
+
+- Improves the new startup messages. See below.
+
+### Bug fixes
+
+- Fixes the new startup messages. See below.
+
+### Improvements and bug fixes to the new startup messages
+
+The two new startup messages introduced in sbt 0.13.15 are:
+
++ when writing out `sbt.version` for build reproducability, and
++ when informing the user sbt shell for the performance improvement
+
+When writing out `sbt.version` the messaging now:
+
++ correctly uses a logger rather than println
++ honours the log level set, for instance, by `--error`
++ never runs when sbt "new" is being run
+
+When informing the user about sbt shell the messaging now:
+
++ is a 1 line message, rather than 3
++ is at info level, rather than warn level
++ can be suppressed with `suppressSbtShellNotification := false`
++ only triggers when "compile" is being run
++ never shows when sbt "new" is being run
+
+[#3091][]/[#3097][]/[#3147][] by [@dwijnand][]
+
+[#3091]: https://github.com/sbt/sbt/issues/3091
+[#3097]: https://github.com/sbt/sbt/issues/3097
+[#3147]: https://github.com/sbt/sbt/pull/3147
+
+[@dwijnand]: https://github.com/dwijnand