diff --git a/src/integrations/terminal/BaseTerminal.ts b/src/integrations/terminal/BaseTerminal.ts
index 121dc343136..7573ca9be6c 100644
--- a/src/integrations/terminal/BaseTerminal.ts
+++ b/src/integrations/terminal/BaseTerminal.ts
@@ -40,11 +40,16 @@ export abstract class BaseTerminal implements RooTerminal {
 	abstract runCommand(command: string, callbacks: RooTerminalCallbacks): RooTerminalProcessResultPromise
 
 	/**
-	 * Sets the active stream for this terminal and notifies the process
+	 * Sets the active stream for this terminal and notifies the process.
+	 * When eventCommand is provided, the stream is only set if it matches the process's command.
+	 * This prevents conda/other auto-activation commands from interfering with Roo's command execution.
+	 *
 	 * @param stream The stream to set, or undefined to clean up
+	 * @param pid The process ID from the shell execution event
+	 * @param eventCommand The command from the shell execution event, used to verify this is Roo's command
 	 * @throws Error if process is undefined when a stream is provided
 	 */
-	public setActiveStream(stream: AsyncIterable<string> | undefined, pid?: number): void {
+	public setActiveStream(stream: AsyncIterable<string> | undefined, pid?: number, eventCommand?: string): void {
 		if (stream) {
 			if (!this.process) {
 				this.running = false
@@ -56,6 +61,18 @@ export abstract class BaseTerminal implements RooTerminal {
 				return
 			}
 
+			// If eventCommand is provided, verify it matches the process's expected command
+			// This prevents conda/pyenv/other auto-activation commands from hijacking the stream
+			if (eventCommand !== undefined && this.process.command) {
+				if (!BaseTerminal.commandsMatch(this.process.command, eventCommand)) {
+					console.debug(
+						`[Terminal ${this.provider}/${this.id}] Ignoring shell execution for non-matching command. ` +
+							`Expected: "${this.process.command}", Got: "${eventCommand}"`,
+					)
+					return
+				}
+			}
+
 			this.running = true
 			this.streamClosed = false
 			this.process.emit("shell_execution_started", pid)
@@ -65,6 +82,39 @@ export abstract class BaseTerminal implements RooTerminal {
 		}
 	}
 
+	/**
+	 * Checks if two commands match. Uses flexible matching to handle cases where
+	 * the executed command might be modified (e.g., PowerShell counter workaround).
+	 *
+	 * @param expectedCommand The command Roo is trying to execute
+	 * @param actualCommand The command from the shell execution event
+	 * @returns true if the commands match
+	 */
+	public static commandsMatch(expectedCommand: string, actualCommand: string): boolean {
+		// Normalize commands by trimming whitespace
+		const expected = expectedCommand.trim()
+		const actual = actualCommand.trim()
+
+		// Exact match (handles both empty string case and exact matches)
+		if (expected === actual) {
+			return true
+		}
+
+		// If expected is empty but actual is not, they don't match
+		// (this prevents empty process command from matching any event command)
+		if (expected.length === 0) {
+			return false
+		}
+
+		// Check if expected is a prefix of actual (handles PowerShell counter workaround
+		// which appends extra commands like ` ; "(Roo/PS Workaround: N)" > $null`)
+		if (actual.startsWith(expected)) {
+			return true
+		}
+
+		return false
+	}
+
 	/**
 	 * Handles shell execution completion for this terminal.
 	 * @param exitDetails The exit details of the shell execution
diff --git a/src/integrations/terminal/TerminalRegistry.ts b/src/integrations/terminal/TerminalRegistry.ts
index 6e0531bebe8..4e6ea569926 100644
--- a/src/integrations/terminal/TerminalRegistry.ts
+++ b/src/integrations/terminal/TerminalRegistry.ts
@@ -51,14 +51,19 @@ export class TerminalRegistry {
 					// Get a handle to the stream as early as possible:
 					const stream = e.execution.read()
 					const terminal = this.getTerminalByVSCETerminal(e.terminal)
+					const eventCommand = e.execution?.commandLine?.value
 
 					console.info("[onDidStartTerminalShellExecution]", {
-						command: e.execution?.commandLine?.value,
+						command: eventCommand,
 						terminalId: terminal?.id,
+						processCommand: terminal?.process?.command,
 					})
 
 					if (terminal) {
-						terminal.setActiveStream(stream)
+						// Pass the eventCommand to setActiveStream for verification.
+						// This prevents conda/pyenv/other auto-activation commands from
+						// hijacking the stream when the terminal first opens.
+						terminal.setActiveStream(stream, undefined, eventCommand)
 						terminal.busy = true // Mark terminal as busy when shell execution starts
 					} else {
 						console.error(
diff --git a/src/integrations/terminal/__tests__/BaseTerminal.spec.ts b/src/integrations/terminal/__tests__/BaseTerminal.spec.ts
new file mode 100644
index 00000000000..299db35b1e6
--- /dev/null
+++ b/src/integrations/terminal/__tests__/BaseTerminal.spec.ts
@@ -0,0 +1,216 @@
+// npx vitest run src/integrations/terminal/__tests__/BaseTerminal.spec.ts
+
+import { BaseTerminal } from "../BaseTerminal"
+import type { RooTerminalProcess } from "../types"
+
+// Create a concrete implementation of BaseTerminal for testing
+class TestTerminal extends BaseTerminal {
+	constructor(id: number = 1, cwd: string = "/test") {
+		super("vscode", id, cwd)
+	}
+
+	isClosed(): boolean {
+		return false
+	}
+
+	runCommand(): never {
+		throw new Error("Not implemented")
+	}
+}
+
+// Create a mock process for testing
+function createMockProcess(command: string): RooTerminalProcess {
+	const events: Record<string, ((...args: any[]) => void)[]> = {}
+
+	return {
+		command,
+		isHot: false,
+		run: vi.fn(),
+		continue: vi.fn(),
+		abort: vi.fn(),
+		hasUnretrievedOutput: vi.fn().mockReturnValue(false),
+		getUnretrievedOutput: vi.fn().mockReturnValue(""),
+		trimRetrievedOutput: vi.fn(),
+		on: vi.fn((event: string, handler: (...args: any[]) => void) => {
+			if (!events[event]) {
+				events[event] = []
+			}
+			events[event].push(handler)
+		}),
+		once: vi.fn((event: string, handler: (...args: any[]) => void) => {
+			if (!events[event]) {
+				events[event] = []
+			}
+			events[event].push(handler)
+		}),
+		emit: vi.fn((event: string, ...args: any[]) => {
+			const handlers = events[event] || []
+			handlers.forEach((handler) => handler(...args))
+			return true
+		}),
+		off: vi.fn(),
+		removeListener: vi.fn(),
+		removeAllListeners: vi.fn(),
+		listeners: vi.fn(),
+		rawListeners: vi.fn(),
+		listenerCount: vi.fn(),
+		prependListener: vi.fn(),
+		prependOnceListener: vi.fn(),
+		eventNames: vi.fn(),
+		addListener: vi.fn(),
+		setMaxListeners: vi.fn(),
+		getMaxListeners: vi.fn(),
+	} as unknown as RooTerminalProcess
+}
+
+// Create a mock async iterable stream for testing
+async function* createMockStream(): AsyncGenerator<string> {
+	yield "test output"
+}
+
+describe("BaseTerminal", () => {
+	describe("commandsMatch", () => {
+		it("returns true for exact match", () => {
+			expect(BaseTerminal.commandsMatch("npm test", "npm test")).toBe(true)
+		})
+
+		it("returns true for exact match with whitespace trimming", () => {
+			expect(BaseTerminal.commandsMatch("  npm test  ", "npm test")).toBe(true)
+			expect(BaseTerminal.commandsMatch("npm test", "  npm test  ")).toBe(true)
+		})
+
+		it("returns true when actual command starts with expected command (PowerShell workaround)", () => {
+			// PowerShell counter workaround appends extra commands
+			const expected = "npm test"
+			const actual = 'npm test ; "(Roo/PS Workaround: 1)" > $null'
+			expect(BaseTerminal.commandsMatch(expected, actual)).toBe(true)
+		})
+
+		it("returns true when actual command has trailing sleep command", () => {
+			const expected = "npm test"
+			const actual = "npm test ; start-sleep -milliseconds 50"
+			expect(BaseTerminal.commandsMatch(expected, actual)).toBe(true)
+		})
+
+		it("returns false for completely different commands", () => {
+			expect(BaseTerminal.commandsMatch("npm test", "conda activate base")).toBe(false)
+		})
+
+		it("returns false when commands are similar but not matching", () => {
+			expect(BaseTerminal.commandsMatch("npm install", "npm run build")).toBe(false)
+		})
+
+		it("returns false for reversed prefix (actual is prefix of expected)", () => {
+			// This case should not match - the expected command should be a prefix of actual
+			expect(BaseTerminal.commandsMatch("npm test --coverage", "npm test")).toBe(false)
+		})
+
+		it("handles empty strings", () => {
+			expect(BaseTerminal.commandsMatch("", "")).toBe(true)
+			expect(BaseTerminal.commandsMatch("npm test", "")).toBe(false)
+			expect(BaseTerminal.commandsMatch("", "npm test")).toBe(false)
+		})
+
+		it("handles commands with special characters", () => {
+			const expected = 'echo "hello world"'
+			const actual = 'echo "hello world"'
+			expect(BaseTerminal.commandsMatch(expected, actual)).toBe(true)
+		})
+
+		it("handles conda activation commands correctly", () => {
+			// Roo's command should not match conda's auto-activation
+			expect(BaseTerminal.commandsMatch("npm test", "conda activate base")).toBe(false)
+			expect(BaseTerminal.commandsMatch("npm test", "source activate myenv")).toBe(false)
+		})
+	})
+
+	describe("setActiveStream", () => {
+		let terminal: TestTerminal
+		let mockProcess: RooTerminalProcess
+
+		beforeEach(() => {
+			terminal = new TestTerminal()
+			mockProcess = createMockProcess("npm test")
+			terminal.process = mockProcess
+		})
+
+		it("sets stream when no eventCommand is provided (backwards compatibility)", () => {
+			const stream = createMockStream()
+			terminal.setActiveStream(stream)
+
+			expect(terminal.running).toBe(true)
+			expect(mockProcess.emit).toHaveBeenCalledWith("shell_execution_started", undefined)
+			expect(mockProcess.emit).toHaveBeenCalledWith("stream_available", stream)
+		})
+
+		it("sets stream when eventCommand matches process command", () => {
+			const stream = createMockStream()
+			terminal.setActiveStream(stream, undefined, "npm test")
+
+			expect(terminal.running).toBe(true)
+			expect(mockProcess.emit).toHaveBeenCalledWith("stream_available", stream)
+		})
+
+		it("sets stream when eventCommand starts with process command (PowerShell case)", () => {
+			const stream = createMockStream()
+			terminal.setActiveStream(stream, undefined, 'npm test ; "(Roo/PS Workaround: 1)" > $null')
+
+			expect(terminal.running).toBe(true)
+			expect(mockProcess.emit).toHaveBeenCalledWith("stream_available", stream)
+		})
+
+		it("ignores stream when eventCommand does not match process command", () => {
+			const stream = createMockStream()
+			const consoleSpy = vi.spyOn(console, "debug").mockImplementation(() => {})
+
+			terminal.setActiveStream(stream, undefined, "conda activate base")
+
+			expect(terminal.running).toBe(false)
+			expect(mockProcess.emit).not.toHaveBeenCalledWith("stream_available", expect.anything())
+			expect(consoleSpy).toHaveBeenCalledWith(expect.stringContaining("Ignoring shell execution"))
+
+			consoleSpy.mockRestore()
+		})
+
+		it("accepts stream when process has no command set (backward compatibility)", () => {
+			mockProcess.command = ""
+			const stream = createMockStream()
+
+			// When process.command is empty string, the command verification is skipped
+			// for backward compatibility. The process should accept any stream.
+			terminal.setActiveStream(stream, undefined, "conda activate base")
+
+			// Since process.command is empty, no verification is done and stream is accepted
+			expect(terminal.running).toBe(true)
+			expect(mockProcess.emit).toHaveBeenCalledWith("stream_available", stream)
+		})
+
+		it("cleans up when stream is undefined", () => {
+			terminal.setActiveStream(undefined)
+
+			expect(terminal.isStreamClosed).toBe(true)
+		})
+
+		it("handles missing process gracefully", () => {
+			terminal.process = undefined
+			const stream = createMockStream()
+			const consoleSpy = vi.spyOn(console, "warn").mockImplementation(() => {})
+
+			terminal.setActiveStream(stream)
+
+			expect(terminal.running).toBe(false)
+			expect(consoleSpy).toHaveBeenCalledWith(expect.stringContaining("process is undefined"))
+
+			consoleSpy.mockRestore()
+		})
+
+		it("passes pid to shell_execution_started event", () => {
+			const stream = createMockStream()
+			const pid = 12345
+
+			terminal.setActiveStream(stream, pid, "npm test")
+
+			expect(mockProcess.emit).toHaveBeenCalledWith("shell_execution_started", pid)
+		})
+	})
+})
diff --git a/src/integrations/terminal/types.ts b/src/integrations/terminal/types.ts
index a0c5cde5d50..1a30bcc90b2 100644
--- a/src/integrations/terminal/types.ts
+++ b/src/integrations/terminal/types.ts
@@ -12,7 +12,7 @@ export interface RooTerminal {
 	getCurrentWorkingDirectory(): string
 	isClosed: () => boolean
 	runCommand: (command: string, callbacks: RooTerminalCallbacks) => RooTerminalProcessResultPromise
-	setActiveStream(stream: AsyncIterable<string> | undefined, pid?: number): void
+	setActiveStream(stream: AsyncIterable<string> | undefined, pid?: number, eventCommand?: string): void
 	shellExecutionComplete(exitDetails: ExitCodeDetails): void
 	getProcessesWithOutput(): RooTerminalProcess[]
 	getUnretrievedOutput(): string