Quick Answer
Goa for: beaches, nightlife, Portuguese heritage, backpacker culture, and seafood. Kerala for: backwaters, Ayurveda, tea plantations, wildlife, and a more "Indian" experience. Goa is a party; Kerala is a retreat. Both are excellent — the right choice depends on your energy level.
Beaches
Goa has better beaches — longer stretches, more variety (Palolem for chill, Baga for party, Ashwem for quiet), and a beach shack culture that Kerala lacks. Kerala's beaches (Varkala, Kovalam, Marari) are scenic but smaller and less central to the experience. If beaches are your main draw, Goa wins clearly.
Nature & Experiences
Kerala dominates here. Alleppey backwater houseboats, Munnar tea plantations, Periyar wildlife sanctuary with wild elephants, and Wayanad's misty western ghats offer diversity Goa can't match. Goa has Dudhsagar Falls and spice plantations, but its interior is limited. If you want landscapes beyond beaches, Kerala.
Food
Both are outstanding but different. Goa: seafood (fish curry rice, prawn balchão, pork vindaloo), Portuguese-influenced baking, feni spirit. Kerala: sadya (banana leaf feast), Malabar biryani, appam with stew, fresh fish moilee, toddy (palm wine). Kerala's vegetarian food is among India's best. For seafood: Goa. For vegetarian variety: Kerala.
Cost
Both are affordable. Goa is slightly cheaper for accommodation (more budget hostels and beach huts) but drinks cost more in Kerala (alcohol taxes are high). A Kerala houseboat (₹5,000-8,000/night for private) is a splurge but worth it once. Daily mid-range budget: Goa ₹2,500-4,000, Kerala ₹3,000-5,000.
Verdict
Solo backpacker or friend group wanting fun? → Goa. Couple on a romantic trip? → Kerala (houseboat + tea plantation). Family with kids? → Kerala (calmer, more wholesome). First time in India? → Goa is an easier introduction. Want a wellness retreat? → Kerala invented Ayurveda. Ideally: do both. Goa (5 days) + Kerala (7 days) is a perfect 2-week Indian coast trip.