diff --git a/packages/jsrepo/src/utils/env.ts b/packages/jsrepo/src/utils/env.ts
index 89a2f4d4..82d82ba2 100644
--- a/packages/jsrepo/src/utils/env.ts
+++ b/packages/jsrepo/src/utils/env.ts
@@ -29,18 +29,105 @@ export function searchForEnvFile(
 }
 
 export function parseEnvVariables(contents: string): Record<string, string> {
-	const lines = contents.split('\n').filter((line) => line.trim().length > 0);
-	return lines.reduce(
-		(acc, line) => {
-			const firstEqualIndex = line.indexOf('=');
-			if (firstEqualIndex === -1) return acc;
-			const name = line.slice(0, firstEqualIndex);
-			const value = line.slice(firstEqualIndex + 1);
-			acc[name] = value ?? '';
-			return acc;
-		},
-		{} as Record<string, string>
-	);
+	const result: Record<string, string> = {};
+	const lines = contents.split('\n');
+	let currentKey: string | null = null;
+	let currentValue: string[] = [];
+
+	for (let i = 0; i < lines.length; i++) {
+		const line = lines[i];
+		if (line === undefined) continue;
+		const trimmedLine = line.trim();
+
+		// If we're continuing a multiline value (previous line ended with backslash)
+		if (currentKey !== null && currentValue.length > 0) {
+			// Check if this line ends with backslash (continues to next line)
+			if (line.trimEnd().endsWith('\\')) {
+				// Remove the trailing backslash and leading whitespace, then continue
+				const continuationLine = line.trimEnd().slice(0, -1).replace(/^\s+/, '');
+				currentValue.push(continuationLine);
+				continue;
+			} else {
+				// Check if this line looks like a new variable
+				// If it does, finalize the multiline value first
+				let looksLikeNewVar = false;
+				if (trimmedLine.length > 0 && !trimmedLine.startsWith('#')) {
+					const firstEqualIndex = line.indexOf('=');
+					if (firstEqualIndex > 0) {
+						const potentialName = line.slice(0, firstEqualIndex).trim();
+						// Check if it looks like a valid variable name (alphanumeric/underscore)
+						if (/^[A-Za-z_][A-Za-z0-9_]*$/.test(potentialName)) {
+							looksLikeNewVar = true;
+						}
+					}
+				}
+				
+				if (looksLikeNewVar) {
+					// Multiline value is complete - finalize it
+					// Remove any trailing empty lines
+					while (currentValue.length > 0 && currentValue[currentValue.length - 1] === '') {
+						currentValue.pop();
+					}
+					result[currentKey] = currentValue.join('\n');
+					currentKey = null;
+					currentValue = [];
+					// Continue processing this line as a new variable
+				} else {
+					// Add this line to the multiline value and continue
+					// Only add non-empty lines, or empty lines if we're explicitly continuing
+					const continuationLine = line.replace(/^\s+/, '');
+					currentValue.push(continuationLine);
+					continue;
+				}
+			}
+		}
+
+		// Skip empty lines (only if we're not in a multiline value)
+		if (trimmedLine.length === 0) {
+			continue;
+		}
+
+		// Check for comments
+		if (trimmedLine.startsWith('#')) {
+			continue;
+		}
+
+		const firstEqualIndex = line.indexOf('=');
+		if (firstEqualIndex === -1) {
+			// If we're in a multiline value, this line is a continuation
+			if (currentKey !== null) {
+				currentValue.push(line.replace(/^\s+/, ''));
+				continue;
+			}
+			// Otherwise, skip lines without =
+			continue;
+		}
+
+		const name = line.slice(0, firstEqualIndex).trim();
+		let value = line.slice(firstEqualIndex + 1);
+
+		// Check if line ends with backslash (multiline continuation)
+		if (line.trimEnd().endsWith('\\')) {
+			// Remove the trailing backslash and start building multiline value
+			currentKey = name;
+			currentValue = [value.slice(0, -1).trimEnd()];
+			continue;
+		}
+
+		// Single line value - preserve as-is (including quotes)
+		result[name] = value ?? '';
+	}
+
+	// Handle case where file ends with a multiline value
+	if (currentKey !== null) {
+		// Remove any trailing empty lines
+		while (currentValue.length > 0 && currentValue[currentValue.length - 1] === '') {
+			currentValue.pop();
+		}
+		result[currentKey] = currentValue.join('\n');
+	}
+
+	return result;
 }
 
 export function updateEnvFile(contents: string, envVars: Record<string, string>): string {
diff --git a/packages/jsrepo/tests/utils/env.test.ts b/packages/jsrepo/tests/utils/env.test.ts
index fffef3c1..f2ea2f1d 100644
--- a/packages/jsrepo/tests/utils/env.test.ts
+++ b/packages/jsrepo/tests/utils/env.test.ts
@@ -48,6 +48,57 @@ describe('parseEnvVariables', () => {
 			SIMPLE: 'normal_value',
 		});
 	});
+
+	it('should parse multiline environment variables with backslash continuation', () => {
+		const contents = 'MULTILINE=line1\\\nline2\\\nline3\nSIMPLE=single_line\n';
+		const envVars = parseEnvVariables(contents);
+		expect(envVars).toEqual({
+			MULTILINE: 'line1\nline2\nline3',
+			SIMPLE: 'single_line',
+		});
+	});
+
+	it('should parse multiline environment variables with multiple continuation lines', () => {
+		const contents = 'CERTIFICATE=-----BEGIN CERTIFICATE-----\\\nMIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEA\\\n-----END CERTIFICATE-----\nOTHER=value\n';
+		const envVars = parseEnvVariables(contents);
+		expect(envVars).toEqual({
+			CERTIFICATE: '-----BEGIN CERTIFICATE-----\nMIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEA\n-----END CERTIFICATE-----',
+			OTHER: 'value',
+		});
+	});
+
+	it('should parse multiline environment variables with indentation', () => {
+		const contents = 'MULTILINE=first line\\\n    second line with indent\\\nthird line\n';
+		const envVars = parseEnvVariables(contents);
+		expect(envVars).toEqual({
+			MULTILINE: 'first line\nsecond line with indent\nthird line',
+		});
+	});
+
+	it('should parse multiline environment variables at end of file', () => {
+		const contents = 'MULTILINE=line1\\\nline2\\\nline3';
+		const envVars = parseEnvVariables(contents);
+		expect(envVars).toEqual({
+			MULTILINE: 'line1\nline2\nline3',
+		});
+	});
+
+	it('should handle multiline values with empty continuation lines', () => {
+		const contents = 'MULTILINE=line1\\\n\nline3\n';
+		const envVars = parseEnvVariables(contents);
+		expect(envVars).toEqual({
+			MULTILINE: 'line1\n\nline3',
+		});
+	});
+
+	it('should parse multiline environment variables with quotes preserved', () => {
+		const contents = 'QUOTED="value with quotes"\\\ncontinued\nREGULAR=normal\n';
+		const envVars = parseEnvVariables(contents);
+		expect(envVars).toEqual({
+			QUOTED: '"value with quotes"\ncontinued',
+			REGULAR: 'normal',
+		});
+	});
 });
 
 describe('updateEnvFile', () => {