Chains like Fab India carry organic foods and have stores in several cities. More local organic shops are: 

In Delhi:

• Navdanya Organic Outlet. Stall No. 18, Dilli Haat, New Delhi. 
• Navdanya Organic Cafe. D-26, Hauz Khas, New Delhi
• Navdanya Organic Outlet. 35 Vasant Arcade, Sector B7, Vasant Kunj, Nelson Mandela Marg, New Delhi

In Hyderabad:

Sahaja Aharam:  Organic produce and grains at pick-up points throughout Hyderabad.  To order, call 040-6526 8303 or email  orders@sahajaaharam.in.

In Mumbai:

• Farmer's Market: all kinds of organic fruits, vegetables, grains, oils & snacks.  Sundays in Bandra, Nilgiri Gardens.| Reviews
• Naturally Yours: Good variety of organic foods, oil, produce, etc.  Shop No.3, Ground Floor, Chembur Station Road, Next to Adarsh Hotel, Mumbai, Maharashtra 400071 | Phone: 022 32230003.  Home delivery available.
  
• Borkar farms -- For organic brown rice and mangoes.  Have home delivery in Mumbai. Phone: (022) 251 2471114 / 2453020  Cell: (0) 9820 5500 14.
• Naturebound Farms: Organic Mangoes - you-pick or home delivery.  Contact Ubai Hussein at Dewanmalpada, Katai Village , Biwandi Taluka, Thane | naturebound.farms@gmail.com | Phone  9920018204.
• Dosti foods in Mumbai distributes organic produce such as organic vegetables from Dahanu.  Phone: (022) 20531426, 20531427
• Conscious Foods also supplies Organic Foods in major cities, home delivery in Mumbai
• Khadi Bhandar carries cold pressed oil as well as traditionally harvested honey
• Venkat Iyer ivenkat66@gmail.com – Rice, Moong, groundnuts, cold pressed organic groundnut oil, brown rice poha
• Eco farms 
  Group of thousands of organic farmers, distributes to major cities. Carry organic whole grains and flours - rice, millet, wheat, jowar and mixed flours, as well as channa, tur, urad & mung, whole or split, jaggery, raw sugar, rock salt, peanuts, flax seed, sesame seed, spices and snacks.  Home delivery available.  A-16 Ground Floor, Sagar Tech Plaza, Andheri Kurla Rd, Sakinaka. Phone: 022-28504434 
   
• Navdanya - The Organic Shop
  
  No 10 Mayfair Housing Society
  Oberoi - Raviraj Complex
  Off Andheri Link Road
  Andheri (West)
  Mumbai 400 053.
  Tel: +91 99204 18027
  
  All dry provisions, organic snacks, organic pickles
• Vinita Mathur's- The Health Shop
  New #14
  Peddar Road, Charni Road
  Cumbala Hill
  Mumbai - 400026
  Landmark: Opposite Wama Showroom
  Phone: 022-23524122
  All dry provisions and organic snacks

In Chennai

1. ReStore:  weekly organic produce bazaar in various neighbourhoods in Chennai

2. Arogyam, Centre for Indian Knowledge Systems, +91 4114 230625, 04114-570855 B45
Alagesan Nagar, Opposite Govt. Hospital, Chengalpet - 603001. Organically grown indigenous rice varieties

3. Enfield Agrobase, +91 44 2442 0605. Mangoes, dried bananas, cashew and coconut

4. Future Foods,+91 44 2440 4937. Soya, dals and coffee powder

5. Naturally Auroville, +91 44 3833 0517. Kombucha (a beverage made by fermenting tea and sugar using the yeast kombucha), Spaghetti, ragi, spirulina and bread

6. Ahimsaa Research Foundation, 43 C P Ramaswamy Road, 3rd Floor, Flat No. 12 (Above Mehta Jewellery), R.A. Puram
Phones 2466 2667, 2498 4707

7. Simply mmmm, AnnaNagar (near Blue Star). Organic vegetables available every Saturday and Wednesday, after 2 p.m.

8. Sunday Shandy, +91 44 2499 1203. Weekly fair of organic vegetables, milk and other farm produce, direct from the farm. Every Sunday 9AM to 12PM

9. The Eco Nut, +91 44 2491 9592. Sesame butter and homemade jams

10. Organic milk, +91 44 2499 1203 Murali, New 177, Old 77 Luz Church Road

In Bangalore 

• Navadarshanam (2 hrs from Bangalore) also markets a variety of organic stuff (incl. peanut butter!) 
• Jaivik Mall Lalbagh Bangalore with home delivery run by Jaivik Krishi Society, promoted by Horticulture Dept of state of Karnataka. Phone: 080-65624197.

Link to newspaper article mentioning below Organic Produce Stores in Bangalore

• Adi Naturals, JP Nagar; 26584071


• Era Organics, Sanjaynagar; 9900543881


• Green Channel, Ali Asker Road; 41235739


• Health Food Stores, Sadashiv Nagar; 23601777, 23600630


• Jaiva, Hospital Road; 9448470353


• Khandige, Kanakpura Main Road; 26714599


• Sahaja Samrudhdhi, Sultan Palya; 23650744


• 24 Lettered Mantra, Jayanagar; 4146 7737/38


• Plant rich , Hebbal ; 65302878


• Janodaya, Tel: 23332564


• Jaivika Krishik Society, Lalbagh


• Savayava siri, Rajaji nagar; 22715744


• Iskon’s store – Dharani


• Koshy’s departmentals

Apart from these stores, branded organic food and products like ProNature, Navadarshanam, etc., are available at most super-markets around the city.

  Kerala

Trivandrum

Organic bazaar,
Thanal, H-3,
Jawahar Nagar, Trivandrum
Phone: 2727150, 94473-43520
Every Wednesday and Saturday afternoon (3 Pm to 7 PM)
Monthly bazaar at Chamber of Commerce hall, Jawahar Nagar on every second Saturday ( 1.30 PM to 5.30 PM )
All provisions, oils, seasonal vegetables and fruits
http://www.thanal.org/organicbazaar/

Cochin
Lumiere Organic food and vegetable store
G-268, 11th Cross Road,
Panampilly Nagar, Kochi
Phone 0484- 4012000
All provisions, vegetables , fruits, milk and also has an organic bakery
http://www.lumiere.co.in