Spend the first day in Kochi visiting the Fort Kochi Beach (early morning), Mattancherry Palace (also known as the Dutch Palace), the St. Francis Church, the Chinese Fishing Nets, and finally the Jew Town for some antique shopping. Don't forget to grab a bite of the famous Kochi street-side food and taste their traditional drink, 'Sulaimani'.
Take a morning drive to Alleppey and spend the day exploring the beautiful backwaters. Enjoy a houseboat ride and take in the serene views of Kerala. Visit the Krishnapuram Palace Museum and witness the grandeur of Kerala's architecture. Explore the Marari Beach and enjoy the sunset. Finally, interact with the friendly locals and enjoy the delicious seafood.
On the final day, head to the Alleppey Finishing Point for a shikara ride on the backwaters. Take a walk or cycle around the beautiful lush green paddy fields. Visit the Mullakkal Rajeshwari Temple and offer your prayers. Finally, enjoy some shopping at the Alleppey Canal Market and buy some aromatic spices and organic tea.
If you have more time, visit the Hill Palace Museum and the Kerala Folklore Museum in Kochi. For art lovers, the David Hall Art Gallery and the Vintage Art Gallery are worth the visit. In Alleppey, the Punnamada Lake, the Pathiramanal Island, the Revi Karunakaran Museum, and the Edathua Church are great places to add to your itinerary. If you have less time, skip the shopping in Jew Town and the Alleppey Canal Market, and make sure to spend enough time on the houseboat and the backwaters.