diff --git a/agent/consul/connect_ca_endpoint.go b/agent/consul/connect_ca_endpoint.go
index 47672ee55..4cdb72ff7 100644
--- a/agent/consul/connect_ca_endpoint.go
+++ b/agent/consul/connect_ca_endpoint.go
@@ -5,6 +5,7 @@ import (
 	"fmt"
 	"reflect"
 	"strings"
+	"time"
 
 	"github.com/hashicorp/consul/acl"
 	"github.com/hashicorp/consul/agent/connect"
@@ -177,6 +178,7 @@ func (s *ConnectCA) ConfigurationSet(
 		newRoot := *r
 		if newRoot.Active {
 			newRoot.Active = false
+			newRoot.RotatedOutAt = time.Now()
 		}
 		newRoots = append(newRoots, &newRoot)
 	}
diff --git a/agent/consul/leader.go b/agent/consul/leader.go
index 5fe4eebec..8b32226dc 100644
--- a/agent/consul/leader.go
+++ b/agent/consul/leader.go
@@ -28,7 +28,18 @@ const (
 	barrierWriteTimeout = 2 * time.Minute
 )
 
-var minAutopilotVersion = version.Must(version.NewVersion("0.8.0"))
+var (
+	// caRootPruneInterval is how often we check for stale CARoots to remove.
+	caRootPruneInterval = time.Hour
+
+	// caRootExpireDuration is the duration after which an inactive root is considered
+	// "expired". Currently this is based on the default leaf cert TTL of 3 days.
+	caRootExpireDuration = 7 * 24 * time.Hour
+
+	// minAutopilotVersion is the minimum Consul version in which Autopilot features
+	// are supported.
+	minAutopilotVersion = version.Must(version.NewVersion("0.8.0"))
+)
 
 // monitorLeadership is used to monitor if we acquire or lose our role
 // as the leader in the Raft cluster. There is some work the leader is
@@ -220,6 +231,8 @@ func (s *Server) establishLeadership() error {
 		return err
 	}
 
+	s.startCARootPruning()
+
 	s.setConsistentReadReady()
 	return nil
 }
@@ -236,6 +249,8 @@ func (s *Server) revokeLeadership() error {
 		return err
 	}
 
+	s.stopCARootPruning()
+
 	s.setCAProvider(nil, nil)
 
 	s.resetConsistentReadReady()
@@ -550,6 +565,92 @@ func (s *Server) setCAProvider(newProvider ca.Provider, root *structs.CARoot) {
 	s.caProviderRoot = root
 }
 
+// startCARootPruning starts a goroutine that looks for stale CARoots
+// and removes them from the state store.
+func (s *Server) startCARootPruning() {
+	s.caPruningLock.Lock()
+	defer s.caPruningLock.Unlock()
+
+	if s.caPruningEnabled {
+		return
+	}
+
+	s.caPruningCh = make(chan struct{})
+
+	go func() {
+		ticker := time.NewTicker(caRootPruneInterval)
+		defer ticker.Stop()
+
+		for {
+			select {
+			case <-s.caPruningCh:
+				return
+			case <-ticker.C:
+				if err := s.pruneCARoots(); err != nil {
+					s.logger.Printf("[ERR] connect: error pruning CA roots: %v", err)
+				}
+			}
+		}
+	}()
+
+	s.caPruningEnabled = true
+}
+
+// pruneCARoots looks for any CARoots that have been rotated out and expired.
+func (s *Server) pruneCARoots() error {
+	if !s.config.ConnectEnabled {
+		return nil
+	}
+
+	idx, roots, err := s.fsm.State().CARoots(nil)
+	if err != nil {
+		return err
+	}
+
+	var newRoots structs.CARoots
+	for _, r := range roots {
+		if !r.Active && !r.RotatedOutAt.IsZero() && time.Now().Sub(r.RotatedOutAt) > caRootExpireDuration {
+			s.logger.Printf("[INFO] connect: pruning old unused root CA (ID: %s)", r.ID)
+			continue
+		}
+		newRoot := *r
+		newRoots = append(newRoots, &newRoot)
+	}
+
+	// Return early if there's nothing to remove.
+	if len(newRoots) == len(roots) {
+		return nil
+	}
+
+	// Commit the new root state.
+	var args structs.CARequest
+	args.Op = structs.CAOpSetRoots
+	args.Index = idx
+	args.Roots = newRoots
+	resp, err := s.raftApply(structs.ConnectCARequestType, args)
+	if err != nil {
+		return err
+	}
+	if respErr, ok := resp.(error); ok {
+		return respErr
+	}
+
+	return nil
+}
+
+// stopCARootPruning stops the CARoot pruning process.
+func (s *Server) stopCARootPruning() {
+	s.caPruningLock.Lock()
+	defer s.caPruningLock.Unlock()
+
+	if !s.caPruningEnabled {
+		return
+	}
+
+	close(s.caPruningCh)
+	s.caPruningEnabled = false
+}
+
 // reconcileReaped is used to reconcile nodes that have failed and been reaped
 // from Serf but remain in the catalog. This is done by looking for unknown nodes with serfHealth checks registered.
 // We generate a "reap" event to cause the node to be cleaned up.
diff --git a/agent/consul/leader_test.go b/agent/consul/leader_test.go
index da2092fda..a685223cb 100644
--- a/agent/consul/leader_test.go
+++ b/agent/consul/leader_test.go
@@ -5,12 +5,14 @@ import (
 	"testing"
 	"time"
 
+	"github.com/hashicorp/consul/agent/connect"
 	"github.com/hashicorp/consul/agent/structs"
 	"github.com/hashicorp/consul/api"
 	"github.com/hashicorp/consul/testrpc"
 	"github.com/hashicorp/consul/testutil/retry"
 	"github.com/hashicorp/net-rpc-msgpackrpc"
 	"github.com/hashicorp/serf/serf"
+	"github.com/stretchr/testify/require"
 )
 
 func TestLeader_RegisterMember(t *testing.T) {
@@ -1001,3 +1003,64 @@ func TestLeader_ACL_Initialization(t *testing.T) {
 		})
 	}
 }
+
+func TestLeader_CARootPruning(t *testing.T) {
+	t.Parallel()
+
+	caRootExpireDuration = 500 * time.Millisecond
+	caRootPruneInterval = 200 * time.Millisecond
+
+	require := require.New(t)
+	dir1, s1 := testServer(t)
+	defer os.RemoveAll(dir1)
+	defer s1.Shutdown()
+	codec := rpcClient(t, s1)
+	defer codec.Close()
+
+	testrpc.WaitForLeader(t, s1.RPC, "dc1")
+
+	// Get the current root
+	rootReq := &structs.DCSpecificRequest{
+		Datacenter: "dc1",
+	}
+	var rootList structs.IndexedCARoots
+	require.Nil(msgpackrpc.CallWithCodec(codec, "ConnectCA.Roots", rootReq, &rootList))
+	require.Len(rootList.Roots, 1)
+	oldRoot := rootList.Roots[0]
+
+	// Update the provider config to use a new private key, which should
+	// cause a rotation.
+	_, newKey, err := connect.GeneratePrivateKey()
+	require.NoError(err)
+	newConfig := &structs.CAConfiguration{
+		Provider: "consul",
+		Config: map[string]interface{}{
+			"PrivateKey":     newKey,
+			"RootCert":       "",
+			"RotationPeriod": 90 * 24 * time.Hour,
+		},
+	}
+	{
+		args := &structs.CARequest{
+			Datacenter: "dc1",
+			Config:     newConfig,
+		}
+		var reply interface{}
+
+		require.NoError(msgpackrpc.CallWithCodec(codec, "ConnectCA.ConfigurationSet", args, &reply))
+	}
+
+	// Should have 2 roots now.
+	_, roots, err := s1.fsm.State().CARoots(nil)
+	require.NoError(err)
+	require.Len(roots, 2)
+
+	time.Sleep(caRootExpireDuration * 2)
+
+	// Now the old root should be pruned.
+	_, roots, err = s1.fsm.State().CARoots(nil)
+	require.NoError(err)
+	require.Len(roots, 1)
+	require.True(roots[0].Active)
+	require.NotEqual(roots[0].ID, oldRoot.ID)
+}
diff --git a/agent/consul/server.go b/agent/consul/server.go
index ca363e7a1..4520b1111 100644
--- a/agent/consul/server.go
+++ b/agent/consul/server.go
@@ -107,6 +107,12 @@ type Server struct {
 	caProviderRoot *structs.CARoot
 	caProviderLock sync.RWMutex
 
+	// caPruningCh is used to shut down the CA root pruning goroutine when we
+	// lose leadership.
+	caPruningCh      chan struct{}
+	caPruningLock    sync.RWMutex
+	caPruningEnabled bool
+
 	// Consul configuration
 	config *Config
 
diff --git a/agent/structs/connect_ca.go b/agent/structs/connect_ca.go
index 2577a99a6..375a7df32 100644
--- a/agent/structs/connect_ca.go
+++ b/agent/structs/connect_ca.go
@@ -73,6 +73,11 @@ type CARoot struct {
 	// cannot be active.
 	Active bool
 
+	// RotatedOutAt is the time at which this CA was removed from the state.
+	// This will only be set on roots that have been rotated out from being the
+	// active root.
+	RotatedOutAt time.Time `json:"-"`
+
 	RaftIndex
 }