diff --git a/cmd/server.go b/cmd/server.go
index 0f4a82feb..3d873c5f9 100644
--- a/cmd/server.go
+++ b/cmd/server.go
@@ -44,6 +44,7 @@ const (
 	BitbucketUserFlag          = "bitbucket-user"
 	BitbucketWebhookSecretFlag = "bitbucket-webhook-secret"
 	ConfigFlag                 = "config"
+	CheckoutStrategyFlag       = "checkout-strategy"
 	DataDirFlag                = "data-dir"
 	GHHostnameFlag             = "gh-hostname"
 	GHTokenFlag                = "gh-token"
@@ -64,6 +65,7 @@ const (
 	TFETokenFlag               = "tfe-token"
 
 	// Flag defaults.
+	DefaultCheckoutStrategy = "branch"
 	DefaultBitbucketBaseURL = bitbucketcloud.BaseURL
 	DefaultDataDir          = "~/.atlantis"
 	DefaultGHHostname       = "github.com"
@@ -103,6 +105,16 @@ var stringFlags = []stringFlag{
 		name:        ConfigFlag,
 		description: "Path to config file. All flags can be set in a YAML config file instead.",
 	},
+	{
+		name: CheckoutStrategyFlag,
+		description: "How to check out pull requests. Accepts either 'branch' (default) or 'merge'." +
+			" If set to branch, Atlantis will check out the source branch of the pull request." +
+			" If set to merge, Atlantis will check out the destination branch of the pull request (ex. master)" +
+			" and then locally perform a git merge of the source branch." +
+			" This effectively means Atlantis operates on the repo as it will look" +
+			" after the pull request is merged.",
+		defaultValue: "branch",
+	},
 	{
 		name:         DataDirFlag,
 		description:  "Path to directory to store Atlantis data.",
@@ -372,6 +384,9 @@ func (s *ServerCmd) run() error {
 }
 
 func (s *ServerCmd) setDefaults(c *server.UserConfig) {
+	if c.CheckoutStrategy == "" {
+		c.CheckoutStrategy = DefaultCheckoutStrategy
+	}
 	if c.DataDir == "" {
 		c.DataDir = DefaultDataDir
 	}
@@ -397,6 +412,10 @@ func (s *ServerCmd) validate(userConfig server.UserConfig) error {
 	if logLevel != "debug" && logLevel != "info" && logLevel != "warn" && logLevel != "error" {
 		return errors.New("invalid log level: not one of debug, info, warn, error")
 	}
+	checkoutStrat := userConfig.CheckoutStrategy
+	if checkoutStrat != "branch" && checkoutStrat != "merge" {
+		return errors.New("invalid checkout strategy: not one of branch or merge")
+	}
 
 	if (userConfig.SSLKeyFile == "") != (userConfig.SSLCertFile == "") {
 		return fmt.Errorf("--%s and --%s are both required for ssl", SSLKeyFileFlag, SSLCertFileFlag)
diff --git a/cmd/server_test.go b/cmd/server_test.go
index 1f827929a..7d49c9172 100644
--- a/cmd/server_test.go
+++ b/cmd/server_test.go
@@ -127,6 +127,14 @@ func TestExecute_ValidateLogLevel(t *testing.T) {
 	Equals(t, "invalid log level: not one of debug, info, warn, error", err.Error())
 }
 
+func TestExecute_ValidateCheckoutStrategy(t *testing.T) {
+	c := setupWithDefaults(map[string]interface{}{
+		cmd.CheckoutStrategyFlag: "invalid",
+	})
+	err := c.Execute()
+	ErrEquals(t, "invalid checkout strategy: not one of branch or merge", err)
+}
+
 func TestExecute_ValidateSSLConfig(t *testing.T) {
 	expErr := "--ssl-key-file and --ssl-cert-file are both required for ssl"
 	cases := []struct {
@@ -331,6 +339,7 @@ func TestExecute_Defaults(t *testing.T) {
 	Ok(t, err)
 	Equals(t, dataDir, passedConfig.DataDir)
 
+	Equals(t, "branch", passedConfig.CheckoutStrategy)
 	Equals(t, "github.com", passedConfig.GithubHostname)
 	Equals(t, "token", passedConfig.GithubToken)
 	Equals(t, "user", passedConfig.GithubUser)
@@ -432,6 +441,7 @@ func TestExecute_Flags(t *testing.T) {
 		cmd.BitbucketTokenFlag:         "bitbucket-token",
 		cmd.BitbucketUserFlag:          "bitbucket-user",
 		cmd.BitbucketWebhookSecretFlag: "bitbucket-secret",
+		cmd.CheckoutStrategyFlag:       "merge",
 		cmd.DataDirFlag:                "/path",
 		cmd.GHHostnameFlag:             "ghhostname",
 		cmd.GHTokenFlag:                "token",
@@ -460,6 +470,7 @@ func TestExecute_Flags(t *testing.T) {
 	Equals(t, "bitbucket-token", passedConfig.BitbucketToken)
 	Equals(t, "bitbucket-user", passedConfig.BitbucketUser)
 	Equals(t, "bitbucket-secret", passedConfig.BitbucketWebhookSecret)
+	Equals(t, "merge", passedConfig.CheckoutStrategy)
 	Equals(t, "/path", passedConfig.DataDir)
 	Equals(t, "ghhostname", passedConfig.GithubHostname)
 	Equals(t, "token", passedConfig.GithubToken)
@@ -489,6 +500,7 @@ bitbucket-base-url: "https://mydomain.com"
 bitbucket-token: "bitbucket-token"
 bitbucket-user: "bitbucket-user"
 bitbucket-webhook-secret: "bitbucket-secret"
+checkout-strategy: "merge"
 data-dir: "/path"
 gh-hostname: "ghhostname"
 gh-token: "token"
@@ -521,6 +533,7 @@ tfe-token: my-token
 	Equals(t, "bitbucket-token", passedConfig.BitbucketToken)
 	Equals(t, "bitbucket-user", passedConfig.BitbucketUser)
 	Equals(t, "bitbucket-secret", passedConfig.BitbucketWebhookSecret)
+	Equals(t, "merge", passedConfig.CheckoutStrategy)
 	Equals(t, "/path", passedConfig.DataDir)
 	Equals(t, "ghhostname", passedConfig.GithubHostname)
 	Equals(t, "token", passedConfig.GithubToken)
@@ -550,6 +563,7 @@ bitbucket-base-url: "https://mydomain.com"
 bitbucket-token: "bitbucket-token"
 bitbucket-user: "bitbucket-user"
 bitbucket-webhook-secret: "bitbucket-secret"
+checkout-strategy: "merge"
 data-dir: "/path"
 gh-hostname: "ghhostname"
 gh-token: "token"
@@ -578,6 +592,7 @@ ssl-key-file: my-token
 		"BITBUCKET_TOKEN":          "override-bitbucket-token",
 		"BITBUCKET_USER":           "override-bitbucket-user",
 		"BITBUCKET_WEBHOOK_SECRET": "override-bitbucket-secret",
+		"CHECKOUT_STRATEGY":        "branch",
 		"DATA_DIR":                 "/override-path",
 		"GH_HOSTNAME":              "override-gh-hostname",
 		"GH_TOKEN":                 "override-gh-token",
@@ -610,6 +625,7 @@ ssl-key-file: my-token
 	Equals(t, "override-bitbucket-token", passedConfig.BitbucketToken)
 	Equals(t, "override-bitbucket-user", passedConfig.BitbucketUser)
 	Equals(t, "override-bitbucket-secret", passedConfig.BitbucketWebhookSecret)
+	Equals(t, "branch", passedConfig.CheckoutStrategy)
 	Equals(t, "/override-path", passedConfig.DataDir)
 	Equals(t, "override-gh-hostname", passedConfig.GithubHostname)
 	Equals(t, "override-gh-token", passedConfig.GithubToken)
@@ -639,6 +655,7 @@ bitbucket-base-url: "https://bitbucket-base-url"
 bitbucket-token: "bitbucket-token"
 bitbucket-user: "bitbucket-user"
 bitbucket-webhook-secret: "bitbucket-secret"
+checkout-strategy: "merge"
 data-dir: "/path"
 gh-hostname: "ghhostname"
 gh-token: "token"
@@ -667,6 +684,7 @@ tfe-token: my-token
 		cmd.BitbucketTokenFlag:         "override-bitbucket-token",
 		cmd.BitbucketUserFlag:          "override-bitbucket-user",
 		cmd.BitbucketWebhookSecretFlag: "override-bitbucket-secret",
+		cmd.CheckoutStrategyFlag:       "branch",
 		cmd.DataDirFlag:                "/override-path",
 		cmd.GHHostnameFlag:             "override-gh-hostname",
 		cmd.GHTokenFlag:                "override-gh-token",
@@ -693,6 +711,7 @@ tfe-token: my-token
 	Equals(t, "override-bitbucket-token", passedConfig.BitbucketToken)
 	Equals(t, "override-bitbucket-user", passedConfig.BitbucketUser)
 	Equals(t, "override-bitbucket-secret", passedConfig.BitbucketWebhookSecret)
+	Equals(t, "branch", passedConfig.CheckoutStrategy)
 	Equals(t, "/override-path", passedConfig.DataDir)
 	Equals(t, "override-gh-hostname", passedConfig.GithubHostname)
 	Equals(t, "override-gh-token", passedConfig.GithubToken)
@@ -723,6 +742,7 @@ func TestExecute_FlagEnvVarOverride(t *testing.T) {
 		"BITBUCKET_TOKEN":          "bitbucket-token",
 		"BITBUCKET_USER":           "bitbucket-user",
 		"BITBUCKET_WEBHOOK_SECRET": "bitbucket-secret",
+		"CHECKOUT_STRATEGY":        "merge",
 		"DATA_DIR":                 "/path",
 		"GH_HOSTNAME":              "gh-hostname",
 		"GH_TOKEN":                 "gh-token",
@@ -759,6 +779,7 @@ func TestExecute_FlagEnvVarOverride(t *testing.T) {
 		cmd.BitbucketTokenFlag:         "override-bitbucket-token",
 		cmd.BitbucketUserFlag:          "override-bitbucket-user",
 		cmd.BitbucketWebhookSecretFlag: "override-bitbucket-secret",
+		cmd.CheckoutStrategyFlag:       "branch",
 		cmd.DataDirFlag:                "/override-path",
 		cmd.GHHostnameFlag:             "override-gh-hostname",
 		cmd.GHTokenFlag:                "override-gh-token",
@@ -787,6 +808,7 @@ func TestExecute_FlagEnvVarOverride(t *testing.T) {
 	Equals(t, "override-bitbucket-token", passedConfig.BitbucketToken)
 	Equals(t, "override-bitbucket-user", passedConfig.BitbucketUser)
 	Equals(t, "override-bitbucket-secret", passedConfig.BitbucketWebhookSecret)
+	Equals(t, "branch", passedConfig.CheckoutStrategy)
 	Equals(t, "/override-path", passedConfig.DataDir)
 	Equals(t, "override-gh-hostname", passedConfig.GithubHostname)
 	Equals(t, "override-gh-token", passedConfig.GithubToken)
diff --git a/server/events/working_dir.go b/server/events/working_dir.go
index b00ab31af..c25e08efb 100644
--- a/server/events/working_dir.go
+++ b/server/events/working_dir.go
@@ -14,6 +14,7 @@
 package events
 
 import (
+	"fmt"
 	"os"
 	"os/exec"
 	"path/filepath"
@@ -46,6 +47,11 @@ type WorkingDir interface {
 // FileWorkspace implements WorkingDir with the file system.
 type FileWorkspace struct {
 	DataDir string
+	// CheckoutMerge is true if we should check out the branch that corresponds
+	// to what the base branch will look like *after* the pull request is merged.
+	// If this is false, then we will check out the head branch from the pull
+	// request.
+	CheckoutMerge bool
 	// TestingOverrideCloneURL can be used during testing to override the URL
 	// that is cloned. If it's empty then we clone normally.
 	TestingOverrideCloneURL string
@@ -67,11 +73,21 @@ func (w *FileWorkspace) Clone(
 	// If so, then we do nothing.
 	if _, err := os.Stat(cloneDir); err == nil {
 		log.Debug("clone directory %q already exists, checking if it's at the right commit", cloneDir)
-		revParseCmd := exec.Command("git", "rev-parse", "HEAD") // #nosec
+
+		// We use git rev-parse to see if our repo is at the right commit.
+		// If just checking out the pull request branch, we can use HEAD.
+		// If doing a merge, then HEAD won't be at the pull request's HEAD
+		// because we'll already have performed a merge. Instead, we'll check
+		// HEAD^2 since that will be the commit before our merge.
+		pullHead := "HEAD"
+		if w.CheckoutMerge {
+			pullHead = "HEAD^2"
+		}
+		revParseCmd := exec.Command("git", "rev-parse", pullHead) // #nosec
 		revParseCmd.Dir = cloneDir
 		output, err := revParseCmd.CombinedOutput()
 		if err != nil {
-			log.Err("will re-clone repo, could not determine if was at correct commit: git rev-parse HEAD: %s: %s", err, string(output))
+			log.Err("will re-clone repo, could not determine if was at correct commit: %s: %s: %s", strings.Join(revParseCmd.Args, " "), err, string(output))
 			return w.forceClone(log, cloneDir, headRepo, p)
 		}
 		currCommit := strings.Trim(string(output), "\n")
@@ -105,22 +121,48 @@ func (w *FileWorkspace) forceClone(log *logging.SimpleLogger,
 		return "", errors.Wrap(err, "creating new workspace")
 	}
 
-	log.Info("git cloning %q into %q", headRepo.SanitizedCloneURL, cloneDir)
-	cloneURL := headRepo.CloneURL
-	if w.TestingOverrideCloneURL != "" {
-		cloneURL = w.TestingOverrideCloneURL
-	}
-	cloneCmd := exec.Command("git", "clone", cloneURL, cloneDir) // #nosec
-	if output, err := cloneCmd.CombinedOutput(); err != nil {
-		return "", errors.Wrapf(err, "cloning %s: %s", headRepo.SanitizedCloneURL, string(output))
+	var cmds [][]string
+	if w.CheckoutMerge {
+		// NOTE: We can't do a shallow clone when we're merging because we'll
+		// get merge conflicts if our clone doesn't have the commits that the
+		// branch we're merging branched off at.
+		// See https://groups.google.com/forum/#!topic/git-users/v3MkuuiDJ98.
+		cmds = [][]string{
+			{
+				"git", "clone", "--branch", p.BaseBranch, "--single-branch", p.BaseRepo.CloneURL, cloneDir,
+			},
+			{
+				"git", "remote", "add", "head", headRepo.CloneURL,
+			},
+			{
+				"git", "fetch", "head", fmt.Sprintf("+refs/heads/%s:", p.HeadBranch),
+			},
+			{
+				"git", "merge", "-q", "-m", "atlantis-merge", "FETCH_HEAD",
+			},
+		}
+	} else {
+		cloneURL := headRepo.CloneURL
+		if w.TestingOverrideCloneURL != "" {
+			cloneURL = w.TestingOverrideCloneURL
+		}
+		cmds = [][]string{
+			{
+				"git", "clone", "--branch", p.HeadBranch, "--depth=1", "--single-branch", cloneURL, cloneDir,
+			},
+		}
 	}
 
-	// Check out the branch for this PR.
-	log.Info("checking out branch %q", p.Branch)
-	checkoutCmd := exec.Command("git", "checkout", p.Branch) // #nosec
-	checkoutCmd.Dir = cloneDir
-	if err := checkoutCmd.Run(); err != nil {
-		return "", errors.Wrapf(err, "checking out branch %s", p.Branch)
+	for _, args := range cmds {
+		cmd := exec.Command(args[0], args[1:]...)
+		cmd.Dir = cloneDir
+
+		cmdStr := w.cmdAsSanitizedStr(cmd, p.BaseRepo, headRepo)
+		output, err := cmd.CombinedOutput()
+		if err != nil {
+			return "", errors.Wrapf(err, "running %s: %s", cmdStr, string(output))
+		}
+		log.Debug("ran: %s. Output: %s", cmdStr, string(output))
 	}
 	return cloneDir, nil
 }
@@ -161,3 +203,9 @@ func (w *FileWorkspace) repoPullDir(r models.Repo, p models.PullRequest) string
 func (w *FileWorkspace) cloneDir(r models.Repo, p models.PullRequest, workspace string) string {
 	return filepath.Join(w.repoPullDir(r, p), workspace)
 }
+
+func (w *FileWorkspace) cmdAsSanitizedStr(cmd *exec.Cmd, base models.Repo, head models.Repo) string {
+	cmdAsStr := strings.Join(cmd.Args, " ")
+	baseReplaced := strings.Replace(cmdAsStr, base.CloneURL, base.SanitizedCloneURL, -1)
+	return strings.Replace(baseReplaced, head.CloneURL, head.SanitizedCloneURL, -1)
+}
diff --git a/server/events_controller_e2e_test.go b/server/events_controller_e2e_test.go
index 3de8e7b23..e42658151 100644
--- a/server/events_controller_e2e_test.go
+++ b/server/events_controller_e2e_test.go
@@ -425,6 +425,7 @@ func GitHubPullRequestParsed(headSHA string) *github.PullRequest {
 				FullName: github.String("runatlantis/atlantis-tests"),
 				CloneURL: github.String("/runatlantis/atlantis-tests.git"),
 			},
+			Ref: github.String("master"),
 		},
 		User: &github.User{
 			Login: github.String("atlantisbot"),
diff --git a/server/server.go b/server/server.go
index 957bd2ec6..a21837692 100644
--- a/server/server.go
+++ b/server/server.go
@@ -182,7 +182,8 @@ func NewServer(userConfig UserConfig, config Config) (*Server, error) {
 	lockingClient := locking.NewClient(boltdb)
 	workingDirLocker := events.NewDefaultWorkingDirLocker()
 	workingDir := &events.FileWorkspace{
-		DataDir: userConfig.DataDir,
+		DataDir:       userConfig.DataDir,
+		CheckoutMerge: userConfig.CheckoutStrategy == "merge",
 	}
 	projectLocker := &events.DefaultProjectLocker{
 		Locker: lockingClient,
diff --git a/server/user_config.go b/server/user_config.go
index 6cf174c31..07bf60816 100644
--- a/server/user_config.go
+++ b/server/user_config.go
@@ -13,6 +13,7 @@ type UserConfig struct {
 	BitbucketToken         string `mapstructure:"bitbucket-token"`
 	BitbucketUser          string `mapstructure:"bitbucket-user"`
 	BitbucketWebhookSecret string `mapstructure:"bitbucket-webhook-secret"`
+	CheckoutStrategy       string `mapstructure:"checkout-strategy"`
 	DataDir                string `mapstructure:"data-dir"`
 	GithubHostname         string `mapstructure:"gh-hostname"`
 	GithubToken            string `mapstructure:"gh-token"`