diff --git a/pkg/credentials/factory.go b/pkg/credentials/factory.go
index ca6f1d18..42295fc8 100644
--- a/pkg/credentials/factory.go
+++ b/pkg/credentials/factory.go
@@ -2,6 +2,7 @@ package credentials
 
 import (
 	"context"
+	"strings"
 
 	"github.com/docker/docker-credential-helpers/client"
 	"github.com/gptscript-ai/gptscript/pkg/config"
@@ -13,12 +14,32 @@ type ProgramLoaderRunner interface {
 	Run(ctx context.Context, prg types.Program, input string) (output string, err error)
 }
 
-func NewFactory(ctx context.Context, cfg *config.CLIConfig, plr ProgramLoaderRunner) (StoreFactory, error) {
+func NewFactory(ctx context.Context, cfg *config.CLIConfig, overrides []string, plr ProgramLoaderRunner) (StoreFactory, error) {
+	creds, err := ParseCredentialOverrides(overrides)
+	if err != nil {
+		return StoreFactory{}, err
+	}
+
+	overrideMap := make(map[string]map[string]map[string]string)
+	for k, v := range creds {
+		contextName, toolName, ok := strings.Cut(k, ctxSeparator)
+		if !ok {
+			continue
+		}
+		toolMap, ok := overrideMap[contextName]
+		if !ok {
+			toolMap = make(map[string]map[string]string)
+		}
+		toolMap[toolName] = v
+		overrideMap[contextName] = toolMap
+	}
+
 	toolName := translateToolName(cfg.CredentialsStore)
 	if toolName == config.FileCredHelper {
 		return StoreFactory{
-			file: true,
-			cfg:  cfg,
+			file:      true,
+			cfg:       cfg,
+			overrides: overrideMap,
 		}, nil
 	}
 
@@ -28,10 +49,11 @@ func NewFactory(ctx context.Context, cfg *config.CLIConfig, plr ProgramLoaderRun
 	}
 
 	return StoreFactory{
-		ctx:    ctx,
-		prg:    prg,
-		runner: plr,
-		cfg:    cfg,
+		ctx:       ctx,
+		prg:       prg,
+		runner:    plr,
+		cfg:       cfg,
+		overrides: overrideMap,
 	}, nil
 }
 
@@ -41,6 +63,8 @@ type StoreFactory struct {
 	file   bool
 	runner ProgramLoaderRunner
 	cfg    *config.CLIConfig
+	// That's a lot of maps: context -> toolName -> key -> value
+	overrides map[string]map[string]map[string]string
 }
 
 func (s *StoreFactory) NewStore(credCtxs []string) (CredentialStore, error) {
@@ -48,15 +72,23 @@ func (s *StoreFactory) NewStore(credCtxs []string) (CredentialStore, error) {
 		return nil, err
 	}
 	if s.file {
-		return Store{
-			credCtxs: credCtxs,
-			cfg:      s.cfg,
+		return withOverride{
+			target: Store{
+				credCtxs: credCtxs,
+				cfg:      s.cfg,
+			},
+			overrides:   s.overrides,
+			credContext: credCtxs,
 		}, nil
 	}
-	return Store{
-		credCtxs: credCtxs,
-		cfg:      s.cfg,
-		program:  s.program,
+	return withOverride{
+		target: Store{
+			credCtxs: credCtxs,
+			cfg:      s.cfg,
+			program:  s.program,
+		},
+		overrides:   s.overrides,
+		credContext: credCtxs,
 	}, nil
 }
 
diff --git a/pkg/credentials/overrides.go b/pkg/credentials/overrides.go
new file mode 100644
index 00000000..0911cac5
--- /dev/null
+++ b/pkg/credentials/overrides.go
@@ -0,0 +1,149 @@
+package credentials
+
+import (
+	"context"
+	"fmt"
+	"maps"
+	"os"
+	"strings"
+)
+
+// ParseCredentialOverrides parses a string of credential overrides that the user provided as a command line arg.
+// The format of credential overrides can be one of two things:
+// cred1:ENV1,ENV2 (direct mapping of environment variables)
+// cred1:ENV1=VALUE1,ENV2=VALUE2 (key-value pairs)
+//
+// This function turns it into a map[string]map[string]string like this:
+//
+//	{
+//	  "cred1": {
+//	    "ENV1": "VALUE1",
+//	    "ENV2": "VALUE2",
+//	  }
+//	}
+func ParseCredentialOverrides(overrides []string) (map[string]map[string]string, error) {
+	credentialOverrides := make(map[string]map[string]string)
+
+	for _, o := range overrides {
+		credName, envs, found := strings.Cut(o, ":")
+		if !found {
+			return nil, fmt.Errorf("invalid credential override: %s", o)
+		}
+		envMap, ok := credentialOverrides[credName]
+		if !ok {
+			envMap = make(map[string]string)
+		}
+		for _, env := range strings.Split(envs, ",") {
+			for _, env := range strings.Split(env, "|") {
+				key, value, found := strings.Cut(env, "=")
+				if !found {
+					// User just passed an env var name as the key, so look up the value.
+					value = os.Getenv(key)
+				}
+				envMap[key] = value
+			}
+		}
+		credentialOverrides[credName] = envMap
+	}
+
+	return credentialOverrides, nil
+}
+
+type withOverride struct {
+	target      CredentialStore
+	credContext []string
+	overrides   map[string]map[string]map[string]string
+}
+
+func (w withOverride) Get(ctx context.Context, toolName string) (*Credential, bool, error) {
+	for _, credCtx := range w.credContext {
+		overrides, ok := w.overrides[credCtx]
+		if !ok {
+			continue
+		}
+		override, ok := overrides[toolName]
+		if !ok {
+			continue
+		}
+
+		return &Credential{
+			Context:  credCtx,
+			ToolName: toolName,
+			Type:     CredentialTypeTool,
+			Env:      maps.Clone(override),
+		}, true, nil
+	}
+
+	return w.target.Get(ctx, toolName)
+}
+
+func (w withOverride) Add(ctx context.Context, cred Credential) error {
+	for _, credCtx := range w.credContext {
+		if override, ok := w.overrides[credCtx]; ok {
+			if _, ok := override[cred.ToolName]; ok {
+				return fmt.Errorf("cannot add credential with context %q and tool %q because it is statically configure", cred.Context, cred.ToolName)
+			}
+		}
+	}
+	return w.target.Add(ctx, cred)
+}
+
+func (w withOverride) Refresh(ctx context.Context, cred Credential) error {
+	if override, ok := w.overrides[cred.Context]; ok {
+		if _, ok := override[cred.ToolName]; ok {
+			return nil
+		}
+	}
+	return w.target.Refresh(ctx, cred)
+}
+
+func (w withOverride) Remove(ctx context.Context, toolName string) error {
+	for _, credCtx := range w.credContext {
+		if override, ok := w.overrides[credCtx]; ok {
+			if _, ok := override[toolName]; ok {
+				return fmt.Errorf("cannot remove credential with context %q and tool %q because it is statically configure", credCtx, toolName)
+			}
+		}
+	}
+	return w.target.Remove(ctx, toolName)
+}
+
+func (w withOverride) List(ctx context.Context) ([]Credential, error) {
+	creds, err := w.target.List(ctx)
+	if err != nil {
+		return nil, err
+	}
+
+	added := make(map[string]map[string]bool)
+	for i, cred := range creds {
+		if override, ok := w.overrides[cred.Context]; ok {
+			if _, ok := override[cred.ToolName]; ok {
+				creds[i].Type = CredentialTypeTool
+				creds[i].Env = maps.Clone(override[cred.ToolName])
+			}
+		}
+		tools, ok := added[cred.Context]
+		if !ok {
+			tools = make(map[string]bool)
+		}
+		tools[cred.ToolName] = true
+		added[cred.Context] = tools
+	}
+
+	for _, credCtx := range w.credContext {
+		tools := w.overrides[credCtx]
+		for toolName := range tools {
+			if _, ok := added[credCtx][toolName]; ok {
+				continue
+			}
+			creds = append(creds, Credential{
+				Context:  credCtx,
+				ToolName: toolName,
+				Type:     CredentialTypeTool,
+				Env:      maps.Clone(tools[toolName]),
+			})
+		}
+	}
+
+	return creds, nil
+}
diff --git a/pkg/gptscript/gptscript.go b/pkg/gptscript/gptscript.go
index 6b7ceb04..4669e5ab 100644
--- a/pkg/gptscript/gptscript.go
+++ b/pkg/gptscript/gptscript.go
@@ -124,7 +124,7 @@ func New(ctx context.Context, o ...Options) (*GPTScript, error) {
 		return nil, err
 	}
 
-	storeFactory, err := credentials.NewFactory(ctx, cliCfg, simplerRunner)
+	storeFactory, err := credentials.NewFactory(ctx, cliCfg, opts.Runner.CredentialOverrides, simplerRunner)
 	if err != nil {
 		return nil, err
 	}
diff --git a/pkg/runner/credentials.go b/pkg/runner/credentials.go
deleted file mode 100644
index d2fbb00e..00000000
--- a/pkg/runner/credentials.go
+++ /dev/null
@@ -1,43 +0,0 @@
-package runner
-
-import (
-	"fmt"
-	"os"
-	"strings"
-)
-
-// parseCredentialOverrides parses a string of credential overrides that the user provided as a command line arg.
-// The format of credential overrides can be one of two things:
-// cred1:ENV1,ENV2 (direct mapping of environment variables)
-// cred1:ENV1=VALUE1,ENV2=VALUE2 (key-value pairs)
-//
-// This function turns it into a map[string]map[string]string like this:
-//
-//	{
-//	  "cred1": {
-//	    "ENV1": "VALUE1",
-//	    "ENV2": "VALUE2",
-//	  }
-//	}
-func parseCredentialOverrides(overrides []string) (map[string]map[string]string, error) {
-	credentialOverrides := make(map[string]map[string]string)
-
-	for _, o := range overrides {
-		credName, envs, found := strings.Cut(o, ":")
-		if !found {
-			return nil, fmt.Errorf("invalid credential override: %s", o)
-		}
-		envMap := make(map[string]string)
-		for _, env := range strings.Split(envs, ",") {
-			key, value, found := strings.Cut(env, "=")
-			if !found {
-				// User just passed an env var name as the key, so look up the value.
-				value = os.Getenv(key)
-			}
-			envMap[key] = value
-		}
-		credentialOverrides[credName] = envMap
-	}
-
-	return credentialOverrides, nil
-}
diff --git a/pkg/runner/credentials_test.go b/pkg/runner/credentials_test.go
index c568d6be..74fa9353 100644
--- a/pkg/runner/credentials_test.go
+++ b/pkg/runner/credentials_test.go
@@ -4,6 +4,7 @@ import (
 	"os"
 	"testing"
 
+	"github.com/gptscript-ai/gptscript/pkg/credentials"
 	"github.com/stretchr/testify/require"
 )
 
@@ -119,7 +120,7 @@ func TestParseCredentialOverrides(t *testing.T) {
 				_ = os.Setenv(k, v)
 			}
 
-			out, err := parseCredentialOverrides(tc.in)
+			out, err := credentials.ParseCredentialOverrides(tc.in)
 			if tc.expectErr {
 				require.Error(t, err)
 				return
diff --git a/pkg/runner/runner.go b/pkg/runner/runner.go
index 09b242f7..e2699cf6 100644
--- a/pkg/runner/runner.go
+++ b/pkg/runner/runner.go
@@ -754,7 +754,7 @@ func (r *Runner) handleCredentials(callCtx engine.Context, monitor Monitor, env
 		err           error
 	)
 	if r.credOverrides != nil {
-		credOverrides, err = parseCredentialOverrides(r.credOverrides)
+		credOverrides, err = credentials.ParseCredentialOverrides(r.credOverrides)
 		if err != nil {
 			return nil, fmt.Errorf("failed to parse credential overrides: %w", err)
 		}