The inspections were conducted across Maharashtra on Thursday, covering 86 establishments involved in the storage, sale and delivery of food through online platforms.
The regulator issued 60 improvement notices and ordered the temporary suspension of operations at one facility.
Of the 14 suspended licences, five were linked to Blinkit, five to Zepto and two to Instamart.
Blinkit facilities flagged over hygiene, temperature issues
At a Blinkit facility in Malad West, Mumbai, the FDA suspended the establishment's FSSAI licence after finding multiple violations.
The chiller room was operating at 6°C, which the FDA said was above the prescribed temperature. Inspectors also found that medical examination records were unavailable for around 40 food handlers.
Several workers were reportedly not wearing essential protective gear, including headgear, aprons and gloves.
Another Blinkit facility at Shiv Shakti Heights near Patel Chowk in Ghatkopar was found to have inadequate drainage and waste-disposal arrangements, poor temperature control for frozen products and unprotected lighting fixtures in an unpacked-food storage area.
The facility scored just 34 out of 74 points, or about 46 per cent, during the inspection.
Inspectors also reported a cockroach infestation, damaged ceilings and flooring, poor housekeeping and inadequate segregation of food products.
Zepto facility suspended over expired food
A Zepto facility in Lohegaon, Pune, faced licence suspension after inspectors found several food-safety violations, including food products being stored beyond their declared "Use By" dates.
The facility was also not following FIFO (First In, First Out) and FEFO (First Expiry, First Out) practices, which are designed to ensure older or soon-to-expire food is dispatched first.
The FDA reported unhygienic storage conditions, inadequate pest control, poor personal hygiene and serious deficiencies in temperature control for cold-storage areas.
The regulator said Zepto's response during the subsequent hearing was unsatisfactory. Other Zepto-linked establishments in Mumbai were also served notices.
Instamart sites hit by cockroaches, rodents
Some of the most serious pest-related violations were reported at facilities associated with Instamart.
At Swinsta ENT Pvt Ltd near Warje Jakat Naka in Pune's Karvenagar, the FDA suspended the licence after inspectors found an active cockroach infestation.
The facility was also found to have cold-chain failures, temperature-control problems and significant deficiencies in hygiene and pest-control measures.
At another Instamart-linked facility on Hill Road in Bandra West, Mumbai, inspectors found heavy rodent droppings near food packages.
A lizard infestation, rusted metal racks and other hygiene violations were also reported. The facility scored 63 out of 140 during the inspection.
At a Rajidi Retail facility associated with Instamart in Azad Nagar, Andheri West, inspectors found expired poultry being stored at an incorrect temperature.
The product, identified as Zorabian Chicken Curry Cut, was reportedly being stored at 8°C, instead of the 0°C-4°C range cited by the FDA for the product. The expired stock was discarded immediately.
Another Instamart facility on Mahakali Caves Road in Andheri East was found to have overcrowded storage, no air curtains at the main entrances and food bags placed directly on the floor.
Bollywood cafe raided at film city
The FDA's crackdown also extended beyond quick-commerce warehouses.
Officials raided Bollywood Cafe at Dadasaheb Phalke Film City in Goregaon East, where they found food being prepared in unhygienic conditions.
The inspection reportedly uncovered a severe fly infestation, dirty drains and food being prepared on rusty and unclean food-contact surfaces.
The FDA initiated action against the cafe under Section 69 of the Food Safety and Standards Act.
FDA steps up food safety checks
The inspection drive highlights the growing scrutiny of quick-commerce facilities, where food products are stored and dispatched rapidly from local warehouses to consumers.
The Maharashtra FDA's findings have raised concerns over pest control, cold-chain management, expiry-date monitoring, worker hygiene and storage practices at facilities handling food for online delivery.
With 14 licences suspended and dozens of improvement notices issued, the regulator's action signals increased enforcement against food businesses failing to meet prescribed safety and hygiene standards.