diff --git a/builtin-checkout.c b/builtin-checkout.c
index b121fe56de884867b31aeeb5bd704bdaf0310310..efa1ebfe07f99e5092710fb951f9e23f16dd1b85 100644
--- a/builtin-checkout.c
+++ b/builtin-checkout.c
@@ -5,6 +5,7 @@
 #include "commit.h"
 #include "tree.h"
 #include "tree-walk.h"
+#include "cache-tree.h"
 #include "unpack-trees.h"
 #include "dir.h"
 #include "run-command.h"
@@ -367,14 +368,17 @@ static int merge_working_tree(struct checkout_opts *opts,
 	int ret;
 	struct lock_file *lock_file = xcalloc(1, sizeof(struct lock_file));
 	int newfd = hold_locked_index(lock_file, 1);
+	int reprime_cache_tree = 0;
 
 	if (read_cache() < 0)
 		return error("corrupt index file");
 
+	cache_tree_free(&active_cache_tree);
 	if (opts->force) {
 		ret = reset_tree(new->commit->tree, opts, 1);
 		if (ret)
 			return ret;
+		reprime_cache_tree = 1;
 	} else {
 		struct tree_desc trees[2];
 		struct tree *tree;
@@ -410,7 +414,9 @@ static int merge_working_tree(struct checkout_opts *opts,
 		init_tree_desc(&trees[1], tree->buffer, tree->size);
 
 		ret = unpack_trees(2, trees, &topts);
-		if (ret == -1) {
+		if (ret != -1) {
+			reprime_cache_tree = 1;
+		} else {
 			/*
 			 * Unpack couldn't do a trivial merge; either
 			 * give up or do a real merge, depending on
@@ -454,6 +460,8 @@ static int merge_working_tree(struct checkout_opts *opts,
 		}
 	}
 
+	if (reprime_cache_tree)
+		prime_cache_tree(&active_cache_tree, new->commit->tree);
 	if (write_cache(newfd, active_cache, active_nr) ||
 	    commit_locked_index(lock_file))
 		die("unable to write new index file");
diff --git a/builtin-read-tree.c b/builtin-read-tree.c
index 38fef34d3fb6c24ab89043951f1ecf6c96e9bf51..391d709704320dba7a918fdd79b68c6c604d33b2 100644
--- a/builtin-read-tree.c
+++ b/builtin-read-tree.c
@@ -29,41 +29,6 @@ static int list_tree(unsigned char *sha1)
 	return 0;
 }
 
-static void prime_cache_tree_rec(struct cache_tree *it, struct tree *tree)
-{
-	struct tree_desc desc;
-	struct name_entry entry;
-	int cnt;
-
-	hashcpy(it->sha1, tree->object.sha1);
-	init_tree_desc(&desc, tree->buffer, tree->size);
-	cnt = 0;
-	while (tree_entry(&desc, &entry)) {
-		if (!S_ISDIR(entry.mode))
-			cnt++;
-		else {
-			struct cache_tree_sub *sub;
-			struct tree *subtree = lookup_tree(entry.sha1);
-			if (!subtree->object.parsed)
-				parse_tree(subtree);
-			sub = cache_tree_sub(it, entry.path);
-			sub->cache_tree = cache_tree();
-			prime_cache_tree_rec(sub->cache_tree, subtree);
-			cnt += sub->cache_tree->entry_count;
-		}
-	}
-	it->entry_count = cnt;
-}
-
-static void prime_cache_tree(void)
-{
-	if (!nr_trees)
-		return;
-	active_cache_tree = cache_tree();
-	prime_cache_tree_rec(active_cache_tree, trees[0]);
-
-}
-
 static const char read_tree_usage[] = "git read-tree (<sha> | [[-m [--trivial] [--aggressive] | --reset | --prefix=<prefix>] [-u | -i]] [--exclude-per-directory=<gitignore>] [--index-output=<file>] <sha1> [<sha2> [<sha3>]])";
 
 static struct lock_file lock_file;
@@ -211,7 +176,6 @@ int cmd_read_tree(int argc, const char **argv, const char *unused_prefix)
 		case 3:
 		default:
 			opts.fn = threeway_merge;
-			cache_tree_free(&active_cache_tree);
 			break;
 		}
 
@@ -221,6 +185,7 @@ int cmd_read_tree(int argc, const char **argv, const char *unused_prefix)
 			opts.head_idx = 1;
 	}
 
+	cache_tree_free(&active_cache_tree);
 	for (i = 0; i < nr_trees; i++) {
 		struct tree *tree = trees[i];
 		parse_tree(tree);
@@ -234,11 +199,14 @@ int cmd_read_tree(int argc, const char **argv, const char *unused_prefix)
 	 * "-m ent" or "--reset ent" form), we can obtain a fully
 	 * valid cache-tree because the index must match exactly
 	 * what came from the tree.
+	 *
+	 * The same holds true if we are switching between two trees
+	 * using read-tree -m A B.  The index must match B after that.
 	 */
-	if (nr_trees && !opts.prefix && (!opts.merge || (stage == 2))) {
-		cache_tree_free(&active_cache_tree);
-		prime_cache_tree();
-	}
+	if (nr_trees == 1 && !opts.prefix)
+		prime_cache_tree(&active_cache_tree, trees[0]);
+	else if (nr_trees == 2 && opts.merge)
+		prime_cache_tree(&active_cache_tree, trees[1]);
 
 	if (write_cache(newfd, active_cache, active_nr) ||
 	    commit_locked_index(&lock_file))
diff --git a/cache-tree.c b/cache-tree.c
index 3d8f218a5f9e838b15e1d56113a4dd56904ee544..37bf35e636f0966662416f0693dbea5c1cc73311 100644
--- a/cache-tree.c
+++ b/cache-tree.c
@@ -1,5 +1,6 @@
 #include "cache.h"
 #include "tree.h"
+#include "tree-walk.h"
 #include "cache-tree.h"
 
 #ifndef DEBUG
@@ -591,3 +592,36 @@ int write_cache_as_tree(unsigned char *sha1, int missing_ok, const char *prefix)
 
 	return 0;
 }
+
+static void prime_cache_tree_rec(struct cache_tree *it, struct tree *tree)
+{
+	struct tree_desc desc;
+	struct name_entry entry;
+	int cnt;
+
+	hashcpy(it->sha1, tree->object.sha1);
+	init_tree_desc(&desc, tree->buffer, tree->size);
+	cnt = 0;
+	while (tree_entry(&desc, &entry)) {
+		if (!S_ISDIR(entry.mode))
+			cnt++;
+		else {
+			struct cache_tree_sub *sub;
+			struct tree *subtree = lookup_tree(entry.sha1);
+			if (!subtree->object.parsed)
+				parse_tree(subtree);
+			sub = cache_tree_sub(it, entry.path);
+			sub->cache_tree = cache_tree();
+			prime_cache_tree_rec(sub->cache_tree, subtree);
+			cnt += sub->cache_tree->entry_count;
+		}
+	}
+	it->entry_count = cnt;
+}
+
+void prime_cache_tree(struct cache_tree **it, struct tree *tree)
+{
+	cache_tree_free(it);
+	*it = cache_tree();
+	prime_cache_tree_rec(*it, tree);
+}
diff --git a/cache-tree.h b/cache-tree.h
index cf8b790874c4a4f5890b360c237ccdd4a5a03de4..e95883523633a51f833683e96af1738da2868238 100644
--- a/cache-tree.h
+++ b/cache-tree.h
@@ -1,6 +1,8 @@
 #ifndef CACHE_TREE_H
 #define CACHE_TREE_H
 
+#include "tree.h"
+
 struct cache_tree;
 struct cache_tree_sub {
 	struct cache_tree *cache_tree;
@@ -33,4 +35,6 @@ int cache_tree_update(struct cache_tree *, struct cache_entry **, int, int, int)
 #define WRITE_TREE_PREFIX_ERROR (-3)
 
 int write_cache_as_tree(unsigned char *sha1, int missing_ok, const char *prefix);
+void prime_cache_tree(struct cache_tree **, struct tree *);
+
 #endif