diff --git a/nomad/core_sched.go b/nomad/core_sched.go
index d433a7d15e0..00cae976a71 100644
--- a/nomad/core_sched.go
+++ b/nomad/core_sched.go
@@ -105,20 +105,26 @@ OUTER:
 			continue
 		}
 
+		allEvalsGC := true
 		for _, eval := range evals {
 			gc, allocs, err := c.gcEval(eval, oldThreshold)
-			if err != nil || !gc {
-				// We skip the job because it is not finished if it has
-				// non-terminal allocations.
+			if err != nil {
 				continue OUTER
 			}
 
-			gcEval = append(gcEval, eval.ID)
+			// Update whether all evals GC'd so we know whether to GC the job.
+			allEvalsGC = allEvalsGC && gc
+
+			if gc {
+				gcEval = append(gcEval, eval.ID)
+			}
 			gcAlloc = append(gcAlloc, allocs...)
 		}
 
 		// Job is eligible for garbage collection
-		gcJob = append(gcJob, job.ID)
+		if allEvalsGC {
+			gcJob = append(gcJob, job.ID)
+		}
 	}
 
 	// Fast-path the nothing case
@@ -186,28 +192,10 @@ func (c *CoreScheduler) evalGC(eval *structs.Evaluation) error {
 			return err
 		}
 
-		// If the eval is from a running "batch" job we don't want to garbage
-		// collect its allocations. If there is a long running batch job and its
-		// terminal allocations get GC'd the scheduler would re-run the
-		// allocations.
-		if eval.Type == structs.JobTypeBatch {
-			// Check if the job is running
-			job, err := c.snap.JobByID(eval.JobID)
-			if err != nil {
-				return err
-			}
-
-			// If the job has been deregistered, we want to garbage collect the
-			// allocations and evaluations.
-			if job != nil && len(allocs) != 0 {
-				continue
-			}
-		}
-
 		if gc {
 			gcEval = append(gcEval, eval.ID)
-			gcAlloc = append(gcAlloc, allocs...)
 		}
+		gcAlloc = append(gcAlloc, allocs...)
 	}
 
 	// Fast-path the nothing case
@@ -232,6 +220,24 @@ func (c *CoreScheduler) gcEval(eval *structs.Evaluation, thresholdIndex uint64)
 		return false, nil, nil
 	}
 
+	// If the eval is from a running "batch" job we don't want to garbage
+	// collect its allocations. If there is a long running batch job and its
+	// terminal allocations get GC'd the scheduler would re-run the
+	// allocations.
+	if eval.Type == structs.JobTypeBatch {
+		// Check if the job is running
+		job, err := c.snap.JobByID(eval.JobID)
+		if err != nil {
+			return false, nil, err
+		}
+
+		// If the job has been deregistered, we want to garbage collect the
+		// allocations and evaluations.
+		if job != nil {
+			return false, nil, nil
+		}
+	}
+
 	// Get the allocations by eval
 	allocs, err := c.snap.AllocsByEval(eval.ID)
 	if err != nil {
@@ -241,19 +247,20 @@ func (c *CoreScheduler) gcEval(eval *structs.Evaluation, thresholdIndex uint64)
 	}
 
 	// Scan the allocations to ensure they are terminal and old
+	gcEval := true
+	var gcAllocIDs []string
 	for _, alloc := range allocs {
 		if !alloc.TerminalStatus() || alloc.ModifyIndex > thresholdIndex {
-			return false, nil, nil
+			// Can't GC the evaluation since not all of the allocations are
+			// terminal
+			gcEval = false
+		} else {
+			// The allocation is eligible to be GC'd
+			gcAllocIDs = append(gcAllocIDs, alloc.ID)
 		}
 	}
 
-	allocIds := make([]string, len(allocs))
-	for i, alloc := range allocs {
-		allocIds[i] = alloc.ID
-	}
-
-	// Evaluation is eligible for garbage collection
-	return true, allocIds, nil
+	return gcEval, gcAllocIDs, nil
 }
 
 // evalReap contacts the leader and issues a reap on the passed evals and
@@ -343,6 +350,7 @@ func (c *CoreScheduler) nodeGC(eval *structs.Evaluation) error {
 
 	// Collect the nodes to GC
 	var gcNode []string
+OUTER:
 	for {
 		raw := iter.Next()
 		if raw == nil {
@@ -363,9 +371,14 @@ func (c *CoreScheduler) nodeGC(eval *structs.Evaluation) error {
 			continue
 		}
 
-		// If there are any allocations, skip the node
-		if len(allocs) > 0 {
-			continue
+		// If there are any non-terminal allocations, skip the node. If the node
+		// is terminal and the allocations are not, the scheduler may not have
+		// run yet to transistion the allocs on the node to terminal. We delay
+		// GC'ing until this happens.
+		for _, alloc := range allocs {
+			if !alloc.TerminalStatus() {
+				continue OUTER
+			}
 		}
 
 		// Node is eligible for garbage collection
diff --git a/nomad/core_sched_test.go b/nomad/core_sched_test.go
index 5854f164996..f0d6c4165ec 100644
--- a/nomad/core_sched_test.go
+++ b/nomad/core_sched_test.go
@@ -69,6 +69,83 @@ func TestCoreScheduler_EvalGC(t *testing.T) {
 	}
 }
 
+func TestCoreScheduler_EvalGC_Partial(t *testing.T) {
+	s1 := testServer(t, nil)
+	defer s1.Shutdown()
+	testutil.WaitForLeader(t, s1.RPC)
+
+	// Insert "dead" eval
+	state := s1.fsm.State()
+	eval := mock.Eval()
+	eval.Status = structs.EvalStatusComplete
+	err := state.UpsertEvals(1000, []*structs.Evaluation{eval})
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+
+	// Insert "dead" alloc
+	alloc := mock.Alloc()
+	alloc.EvalID = eval.ID
+	alloc.DesiredStatus = structs.AllocDesiredStatusFailed
+	err = state.UpsertAllocs(1001, []*structs.Allocation{alloc})
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+
+	// Insert "running" alloc
+	alloc2 := mock.Alloc()
+	alloc2.EvalID = eval.ID
+	err = state.UpsertAllocs(1002, []*structs.Allocation{alloc2})
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+
+	// Update the time tables to make this work
+	tt := s1.fsm.TimeTable()
+	tt.Witness(2000, time.Now().UTC().Add(-1*s1.config.EvalGCThreshold))
+
+	// Create a core scheduler
+	snap, err := state.Snapshot()
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+	core := NewCoreScheduler(s1, snap)
+
+	// Attempt the GC
+	gc := s1.coreJobEval(structs.CoreJobEvalGC)
+	gc.ModifyIndex = 2000
+	err = core.Process(gc)
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+
+	// Should not be gone
+	out, err := state.EvalByID(eval.ID)
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+	if out == nil {
+		t.Fatalf("bad: %v", out)
+	}
+
+	outA, err := state.AllocByID(alloc2.ID)
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+	if outA == nil {
+		t.Fatalf("bad: %v", outA)
+	}
+
+	// Should be gone
+	outB, err := state.AllocByID(alloc.ID)
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+	if outB != nil {
+		t.Fatalf("bad: %v", outB)
+	}
+}
+
 func TestCoreScheduler_EvalGC_Batch_NoAllocs(t *testing.T) {
 	s1 := testServer(t, nil)
 	defer s1.Shutdown()
@@ -334,6 +411,108 @@ func TestCoreScheduler_NodeGC(t *testing.T) {
 	}
 }
 
+func TestCoreScheduler_NodeGC_TerminalAllocs(t *testing.T) {
+	s1 := testServer(t, nil)
+	defer s1.Shutdown()
+	testutil.WaitForLeader(t, s1.RPC)
+
+	// Insert "dead" node
+	state := s1.fsm.State()
+	node := mock.Node()
+	node.Status = structs.NodeStatusDown
+	err := state.UpsertNode(1000, node)
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+
+	// Insert a terminal alloc on that node
+	alloc := mock.Alloc()
+	alloc.DesiredStatus = structs.AllocDesiredStatusStop
+	if err := state.UpsertAllocs(1001, []*structs.Allocation{alloc}); err != nil {
+		t.Fatalf("err: %v", err)
+	}
+
+	// Update the time tables to make this work
+	tt := s1.fsm.TimeTable()
+	tt.Witness(2000, time.Now().UTC().Add(-1*s1.config.NodeGCThreshold))
+
+	// Create a core scheduler
+	snap, err := state.Snapshot()
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+	core := NewCoreScheduler(s1, snap)
+
+	// Attempt the GC
+	gc := s1.coreJobEval(structs.CoreJobNodeGC)
+	gc.ModifyIndex = 2000
+	err = core.Process(gc)
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+
+	// Should be gone
+	out, err := state.NodeByID(node.ID)
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+	if out != nil {
+		t.Fatalf("bad: %v", out)
+	}
+}
+
+func TestCoreScheduler_NodeGC_RunningAllocs(t *testing.T) {
+	s1 := testServer(t, nil)
+	defer s1.Shutdown()
+	testutil.WaitForLeader(t, s1.RPC)
+
+	// Insert "dead" node
+	state := s1.fsm.State()
+	node := mock.Node()
+	node.Status = structs.NodeStatusDown
+	err := state.UpsertNode(1000, node)
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+
+	// Insert a running alloc on that node
+	alloc := mock.Alloc()
+	alloc.NodeID = node.ID
+	alloc.DesiredStatus = structs.AllocDesiredStatusRun
+	alloc.ClientStatus = structs.AllocClientStatusRunning
+	if err := state.UpsertAllocs(1001, []*structs.Allocation{alloc}); err != nil {
+		t.Fatalf("err: %v", err)
+	}
+
+	// Update the time tables to make this work
+	tt := s1.fsm.TimeTable()
+	tt.Witness(2000, time.Now().UTC().Add(-1*s1.config.NodeGCThreshold))
+
+	// Create a core scheduler
+	snap, err := state.Snapshot()
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+	core := NewCoreScheduler(s1, snap)
+
+	// Attempt the GC
+	gc := s1.coreJobEval(structs.CoreJobNodeGC)
+	gc.ModifyIndex = 2000
+	err = core.Process(gc)
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+
+	// Should still be here
+	out, err := state.NodeByID(node.ID)
+	if err != nil {
+		t.Fatalf("err: %v", err)
+	}
+	if out == nil {
+		t.Fatalf("bad: %v", out)
+	}
+}
+
 func TestCoreScheduler_NodeGC_Force(t *testing.T) {
 	s1 := testServer(t, nil)
 	defer s1.Shutdown()