diff --git a/blueprint/bootstrap/bootstrap.go b/blueprint/bootstrap/bootstrap.go
index 99d6177..2d979a8 100644
--- a/blueprint/bootstrap/bootstrap.go
+++ b/blueprint/bootstrap/bootstrap.go
@@ -180,7 +180,7 @@
 		buildGoPackage(ctx, g.pkgRoot, g.properties.PkgPath, g.archiveFile,
 			g.properties.Srcs)
 	} else {
-		phonyGoTarget(ctx, g.archiveFile, g.properties.Srcs)
+		phonyGoTarget(ctx, g.archiveFile, g.properties.Srcs, nil)
 	}
 }
 
@@ -241,7 +241,8 @@
 			Inputs:  []string{aoutFile},
 		})
 	} else {
-		phonyGoTarget(ctx, binaryFile, g.properties.Srcs)
+		intermediates := []string{aoutFile, archiveFile}
+		phonyGoTarget(ctx, binaryFile, g.properties.Srcs, intermediates)
 	}
 }
 
@@ -279,7 +280,9 @@
 	})
 }
 
-func phonyGoTarget(ctx blueprint.ModuleContext, target string, srcs []string) {
+func phonyGoTarget(ctx blueprint.ModuleContext, target string, srcs []string,
+	intermediates []string) {
+
 	var depTargets []string
 	ctx.VisitDepsDepthFirstIf(isGoPackageProducer,
 		func(module blueprint.Module) {
@@ -309,6 +312,17 @@
 			Outputs: []string{src},
 		})
 	}
+
+	// If there is no rule to build the intermediate files of a bootstrap go package
+	// the cleanup phase of the primary builder will delete the intermediate files,
+	// forcing an unnecessary rebuild.  Add phony rules for all of them.
+	for _, intermediate := range intermediates {
+		ctx.Build(pctx, blueprint.BuildParams{
+			Rule:    blueprint.Phony,
+			Outputs: []string{intermediate},
+		})
+	}
+
 }
 
 type singleton struct{}
@@ -448,23 +462,22 @@
 	} else {
 		// We're generating a non-bootstrapper Ninja file, so we need to set it
 		// up to depend on the bootstrapper Ninja file.  The build.ninja target
-		// also has an implicit dependency on the primary builder, which will
-		// have a phony dependency on all its sources.  This will cause any
-		// changes to the primary builder's sources to trigger a re-bootstrap
-		// operation, which will rebuild the primary builder.
+		// also has an implicit dependency on the primary builder and all other
+		// bootstrap go binaries, which will have phony dependencies on all of
+		// their sources.  This will cause any changes to a bootstrap binary's
+		// sources to trigger a re-bootstrap operation, which will rebuild the
+		// binary.
 		//
 		// On top of that we need to use the depfile generated by the bigbp
 		// rule.  We do this by depending on that file and then setting up a
 		// phony rule to generate it that uses the depfile.
+		buildNinjaDeps := []string{"$bootstrapCmd", mainNinjaFile}
+		buildNinjaDeps = append(buildNinjaDeps, allGoBinaries...)
 		ctx.Build(pctx, blueprint.BuildParams{
-			Rule:    rebootstrap,
-			Outputs: []string{"build.ninja"},
-			Inputs:  []string{"$bootstrapManifest"},
-			Implicits: []string{
-				"$bootstrapCmd",
-				primaryBuilderFile,
-				mainNinjaFile,
-			},
+			Rule:      rebootstrap,
+			Outputs:   []string{"build.ninja"},
+			Inputs:    []string{"$bootstrapManifest"},
+			Implicits: buildNinjaDeps,
 		})
 
 		ctx.Build(pctx, blueprint.BuildParams{