diff --git a/pkg/kubernetes/kubernetes.go b/pkg/kubernetes/kubernetes.go
index c01444cb8..ecb5dda7d 100644
--- a/pkg/kubernetes/kubernetes.go
+++ b/pkg/kubernetes/kubernetes.go
@@ -2,6 +2,7 @@ package kubernetes
 
 import (
 	"fmt"
+	"regexp"
 	"strings"
 
 	"github.com/Masterminds/semver"
@@ -72,7 +73,7 @@ func New(c v1alpha1.Config) (*Kubernetes, error) {
 
 // ApplyOpts allow set additional parameters for the apply operation
 type ApplyOpts struct {
-	PruneOpts
+	*PruneOpts
 
 	// force allows to ignore checks and force the operation
 	Force bool
@@ -114,7 +115,7 @@ func (k *Kubernetes) Apply(state manifest.List, opts ApplyOpts) error {
 		return nil
 	}
 
-	if err := k.prune(state, opts.PruneOpts); err != nil {
+	if err := k.prune(state, *opts.PruneOpts); err != nil {
 		return errors.Wrap(err, "removing orphaned resources")
 	}
 	return nil
@@ -122,7 +123,7 @@ func (k *Kubernetes) Apply(state manifest.List, opts ApplyOpts) error {
 
 // DiffOpts allow to specify additional parameters for diff operations
 type DiffOpts struct {
-	PruneOpts
+	*PruneOpts
 
 	// Use `diffstat(1)` to create a histogram of the changes instead
 	Summarize bool
@@ -140,7 +141,7 @@ func (k *Kubernetes) Diff(state manifest.List, opts DiffOpts) (*string, error) {
 
 	differs := []Differ{k.differs[strategy]}
 	if opts.PruneOpts.Prune {
-		differs = append(differs, k.diffOrphaned(opts.PruneOpts.AllKinds))
+		differs = append(differs, k.diffOrphaned(opts.PruneOpts.AllKinds, opts.PruneOpts.Targets))
 	}
 
 	diff, err := multiDiff(state, differs)
@@ -198,9 +199,9 @@ func diffParallel(diff Differ, state manifest.List, results chan (*string), errs
 	results <- r
 }
 
-func (k *Kubernetes) diffOrphaned(all bool) Differ {
+func (k *Kubernetes) diffOrphaned(all bool, targets []*regexp.Regexp) Differ {
 	return func(state manifest.List) (*string, error) {
-		orphan, err := k.listOrphaned(state, all)
+		orphan, err := k.listOrphaned(state, all, targets)
 		if err != nil {
 			return nil, err
 		}
@@ -231,10 +232,3 @@ func (k *Kubernetes) diffOrphaned(all bool) Differ {
 func (k *Kubernetes) Info() client.Info {
 	return k.info
 }
-
-func objectspec(m manifest.Manifest) string {
-	return fmt.Sprintf("%s/%s",
-		m.Kind(),
-		m.Metadata().Name(),
-	)
-}
diff --git a/pkg/kubernetes/prune.go b/pkg/kubernetes/prune.go
index ae658d3a2..aa92c5554 100644
--- a/pkg/kubernetes/prune.go
+++ b/pkg/kubernetes/prune.go
@@ -1,8 +1,11 @@
 package kubernetes
 
 import (
+	"regexp"
+
 	"github.com/grafana/tanka/pkg/kubernetes/client"
 	"github.com/grafana/tanka/pkg/kubernetes/manifest"
+	"github.com/grafana/tanka/pkg/kubernetes/util"
 	"github.com/pkg/errors"
 )
 
@@ -48,10 +51,13 @@ type PruneOpts struct {
 
 	// Skip verification and force deleting
 	Force bool
+
+	// Limit the working set to these objects
+	Targets []*regexp.Regexp
 }
 
 func (k *Kubernetes) prune(state manifest.List, opts PruneOpts) error {
-	orphan, err := k.listOrphaned(state, opts.AllKinds)
+	orphan, err := k.listOrphaned(state, opts.AllKinds, opts.Targets)
 	if err != nil {
 		return errors.Wrap(err, "listing orphaned objects")
 	}
@@ -66,7 +72,7 @@ func (k *Kubernetes) prune(state manifest.List, opts PruneOpts) error {
 
 // listOrphaned returns all resources known to the cluster not present in
 // Jsonnet
-func (k *Kubernetes) listOrphaned(state manifest.List, all bool) (orphaned manifest.List, err error) {
+func (k *Kubernetes) listOrphaned(state manifest.List, all bool, targets []*regexp.Regexp) (orphaned manifest.List, err error) {
 	if k.orphaned != nil {
 		return k.orphaned, nil
 	}
@@ -116,6 +122,7 @@ func (k *Kubernetes) listOrphaned(state manifest.List, all bool) (orphaned manif
 		return nil, lastErr
 	}
 
+	orphaned = util.FilterTargets(orphaned, targets)
 	return orphaned, nil
 }
 
diff --git a/pkg/kubernetes/reconcile.go b/pkg/kubernetes/reconcile.go
index 1c2e103e4..ddd1fe7b6 100644
--- a/pkg/kubernetes/reconcile.go
+++ b/pkg/kubernetes/reconcile.go
@@ -8,9 +8,9 @@ import (
 
 	"github.com/pkg/errors"
 	"github.com/stretchr/objx"
-	funk "github.com/thoas/go-funk"
 
 	"github.com/grafana/tanka/pkg/kubernetes/manifest"
+	"github.com/grafana/tanka/pkg/kubernetes/util"
 	"github.com/grafana/tanka/pkg/spec/v1alpha1"
 )
 
@@ -48,18 +48,7 @@ func Reconcile(raw map[string]interface{}, config v1alpha1.Config, targets []*re
 	}
 
 	// optionally filter the working set of objects
-	if len(targets) > 0 {
-		tmp := funk.Filter(out, func(i interface{}) bool {
-			p := objectspec(i.(manifest.Manifest))
-			for _, t := range targets {
-				if t.MatchString(p) {
-					return true
-				}
-			}
-			return false
-		}).([]manifest.Manifest)
-		out = manifest.List(tmp)
-	}
+	out = util.FilterTargets(out, targets)
 
 	// Stable output order
 	sort.SliceStable(out, func(i int, j int) bool {
diff --git a/pkg/kubernetes/util/targetexp.go b/pkg/kubernetes/util/targetexp.go
index 79f1d5c9e..23b027dd0 100644
--- a/pkg/kubernetes/util/targetexp.go
+++ b/pkg/kubernetes/util/targetexp.go
@@ -4,6 +4,9 @@ import (
 	"fmt"
 	"regexp"
 	"strings"
+
+	"github.com/grafana/tanka/pkg/kubernetes/manifest"
+	funk "github.com/thoas/go-funk"
 )
 
 type ErrBadTargetExp struct {
@@ -38,3 +41,29 @@ func MustCompileTargetExps(strs ...string) (exps []*regexp.Regexp) {
 	}
 	return exps
 }
+
+// FilterTargets filters list to only include those matched by targets
+func FilterTargets(list manifest.List, targets []*regexp.Regexp) manifest.List {
+	if len(targets) == 0 {
+		return list
+	}
+
+	tmp := funk.Filter(list, func(i interface{}) bool {
+		p := objectspec(i.(manifest.Manifest))
+		for _, t := range targets {
+			if t.MatchString(p) {
+				return true
+			}
+		}
+		return false
+	}).([]manifest.Manifest)
+
+	return manifest.List(tmp)
+}
+
+func objectspec(m manifest.Manifest) string {
+	return fmt.Sprintf("%s/%s",
+		m.Kind(),
+		m.Metadata().Name(),
+	)
+}
diff --git a/pkg/tanka/tanka.go b/pkg/tanka/tanka.go
index ae23f8d8d..bbf411c1e 100644
--- a/pkg/tanka/tanka.go
+++ b/pkg/tanka/tanka.go
@@ -24,9 +24,13 @@ func parseModifiers(mods []Modifier) *options {
 		mod(o)
 	}
 
+	// finish prune object
+	o.prune.Targets = o.targets
 	o.prune.Force = o.apply.Force
-	o.apply.PruneOpts = o.prune
-	o.diff.PruneOpts = o.prune
+
+	// add finished object to apply and diff (they need this info as well)
+	o.apply.PruneOpts = &o.prune
+	o.diff.PruneOpts = &o.prune
 
 	return o
 }
diff --git a/pkg/tanka/workflow.go b/pkg/tanka/workflow.go
index 5ef45fce3..6f541ac8b 100644
--- a/pkg/tanka/workflow.go
+++ b/pkg/tanka/workflow.go
@@ -27,9 +27,7 @@ func Apply(baseDir string, mods ...Modifier) error {
 		return err
 	}
 
-	diff, err := kube.Diff(p.Resources, kubernetes.DiffOpts{
-		PruneOpts: opts.prune,
-	})
+	diff, err := kube.Diff(p.Resources, kubernetes.DiffOpts{})
 	if err != nil {
 		return errors.Wrap(err, "diffing")
 	}