Once you get comfortable with Claude Code, one agent stops being enough. You want one refactoring a module, another writing tests, a third scaffolding a new service - all at once. Running them in parallel is easy. Keeping them isolated, and knowing which one actually needs you, is the hard part.
Here's how to run several Claude Code sessions side by side on Windows without them stepping on each other, and without babysitting a wall of terminals.
Spin up three or four terminals and two problems appear immediately:
The result is that "parallel" work turns into constant context-switching - the opposite of what you wanted.
Claude Desktop Manager lets you create a profile per workstream, each with its own isolated data directory and its own Claude Code configuration. From any profile you open a per-profile terminal in one click - it starts with that profile's own settings and MCP servers, not a shared global set. Two agents can use completely different tools without ever colliding.
Isolation matters more with agents. An autonomous agent that can edit files and call tools is exactly the thing you don't want sharing a config with three other agents. One profile per session keeps each one's MCP set, settings and credentials to itself.
The Claude Code Sessions board shows all your running sessions in one place, with a live status for each: working, waiting for you, done, or stalled. Instead of cycling through terminals to see who needs input, you glance at the board and go straight to the one that does.
For long-running tasks you don't want to watch, Claude Desktop Manager can notify you the moment a session completes. It merges a reversible, idempotent Stop hook into the profile's own Claude Code settings - so when that agent stops, you get an alert and can move to the next one. There's a Do-Not-Disturb mode for when you want the board quiet.
If you also run Claude Desktop alongside these terminals, the same isolation model applies - see running Claude Desktop and Claude Code together. And to give each session its own tools, see MCP servers per profile.
Yes. Claude Code can run in several terminals at the same time. The hard part is keeping them isolated and knowing which one needs you. Claude Desktop Manager launches each session against a profile's own isolated config and shows a live board of which agent is working, waiting, done or stalled.
Give each session its own profile. In Claude Desktop Manager, every profile has an isolated data directory and its own Claude Code configuration, so parallel sessions do not share MCP servers, settings or credentials. You open each one's terminal in a click.
Claude Desktop Manager can notify you when a Claude Code session finishes, via a reversible Stop hook it merges into the profile's settings. A live board shows each agent's state - working, waiting for you, done or stalled - so you are not babysitting terminals.
The per-profile terminal, isolated configs, the Claude Code session board and completion notifications are available across tiers. Simultaneous-instance limits differ by tier: Free allows one at a time, Standard two, and Pro removes the limit.
Claude Desktop Manager is free to download. Standard ($10, one-time purchase) unlocks 2 simultaneous instances with no time limit. Pro ($30, one-time) removes all limits and adds QuickPrompt and QuickAsk.