"Does lemon juice or vinegar in a marinade kill bacteria?"

"Not at the concentrations used in marinades. To reliably reduce Salmonella or E. coli to safe levels using acid alone, you'd need a very high concentration of acid maintained for extended time — conditions that would make the food inedible. A standard marinade with citrus juice or vinegar changes flavor and denatures surface proteins, but it doesn't sterilize the meat. Refrigerator temperature is still required."

"Can I marinate meat overnight?"

"Yes, in the refrigerator. Overnight marinating in the fridge (8-12 hours) is safe and often desirable for flavor development. Don't go beyond 2 days for most meats, and keep chicken to 2 days maximum — acid begins to break down surface proteins, creating a mushy or mealy texture. Beef and lamb can tolerate longer marination. Fish should be marinated for no more than 30-60 minutes in an acid marinade because delicate proteins break down quickly."

"What do I do if I marinated meat at room temperature by accident?"

"The USDA 2-hour rule applies. If the meat was at room temperature (above 40°F) for less than 2 hours, cook it promptly to the appropriate internal temperature. More than 2 hours: discard it. Bacteria like Salmonella and Campylobacter can multiply rapidly in the danger zone and reach infectious levels within 2-4 hours. Cooking kills bacteria, but Staph aureus toxins (which can form during extended room-temperature holding) survive cooking."

"Can enzyme marinades (papaya, pineapple, kiwi) substitute for refrigerator time?"

"No. Enzyme tenderizers (papain from papaya, bromelain from pineapple, actinidin from kiwi) are effective tenderizers but they work on proteins from the surface in, not on pathogens throughout. They don't kill bacteria. Extended enzyme marination at room temperature still puts the meat in the danger zone. Keep enzyme marinades refrigerated too — but don't over-marinate, as these enzymes can turn the surface to mush."

Marinating Meat Safely: What Temperature Rules Apply and What Doesn't Work

Quick Answer

Marinate raw meat in the refrigerator, always. Acid in marinades (vinegar, citrus, wine) changes texture and flavor but doesn't kill pathogens at safe, palatable concentrations. Marinade that touches raw meat is contaminated and can't be reused on cooked food unless boiled to 165°F first.

The Science

People marinate meat at room temperature all the time. It’s often presented in cookbooks as a step — set it on the counter and let it marinate for an hour before cooking. It’s also a food safety mistake.

The logic behind room-temperature marinating is usually one of two things: either “the acid will kill the bacteria” or “it’ll only be an hour, it’ll be fine.” Neither holds up.

The Danger Zone Still Applies

The temperature danger zone is 40 to 140°F. Bacteria like Salmonella, Campylobacter, and E. coli multiply rapidly in this range. Under ideal conditions, bacterial populations can double every 20 minutes.

A raw chicken breast marinating on the counter at room temperature is raw chicken breast in the danger zone. The marinade doesn’t change that calculation. The acid in the marinade — vinegar, lemon juice, wine, yogurt — modifies the surface proteins of the meat, which changes texture and how flavors bind. It does not sterilize the meat.

The USDA’s position is clear: marinate in the refrigerator, not on the counter.

Why Acid Doesn’t Kill Pathogens in Marinade

This is the most persistent misconception in home cooking. The belief that vinegar or citrus juice kills bacteria is based on the correct fact that high acid concentrations are lethal to bacteria. The error is in the dose.

Acidic conditions (pH below 4.0) inhibit and eventually kill bacteria over time. But “palatable marinade” and “bactericidal acid concentration” don’t overlap.

A typical citrus or vinegar marinade has a pH of around 3.5 to 4.5 — acidic, but not uniformly so after diluting with oil, garlic, herbs, and the moisture released from the meat. Researchers studying acid treatments for pathogen reduction use much higher concentrations, much longer contact times, or both.

Citrus ceviche marinades are a related example. The “cooked by lime juice” effect that turns raw fish opaque is protein denaturation, not pathogen kill. Anisakis larvae survive lime juice. Some bacterial pathogens survive the acid concentrations and times used in typical ceviche preparation.

The acid-base cooking article explains the chemistry of acid on food proteins in more depth. The short version: acid changes structure without necessarily killing everything living in the food.

Marinade Reuse: The Cross-Contamination Risk

Once marinade has touched raw meat, it’s contaminated with whatever pathogens were on or in that meat. Salmonella, Campylobacter, and E. coli can be present in marinade after it contacts raw chicken or beef.

Using that marinade as a sauce — basting during cooking, serving alongside the cooked meat — transfers those pathogens directly to the finished dish.

Two safe approaches:

Set aside a portion of the marinade before it contacts raw meat. This portion is clean and safe to use as sauce.
Boil the used marinade for at least several minutes, reaching 165°F, to kill any contamination. Then it’s safe to use as sauce.

Never pour the used marinade over cooked food without one of those two steps. The cross-contamination article covers the broader picture of how pathogens transfer from raw to cooked surfaces.

Enzyme Tenderizers: Different Chemistry, Same Temperature Rules

Enzyme-based marinades work differently from acid marinades. Papain (from papaya), bromelain (from pineapple), and actinidin (from kiwi) are proteolytic enzymes — they break peptide bonds in meat proteins, softening muscle structure.

These enzymes are effective tenderizers, but they’re not antiseptics. They work from the surface inward, which is why over-marinating creates a mealy, unpleasantly soft exterior: the enzyme activity is most intense at the meat surface and lessens with depth. They don’t kill bacteria.

And enzyme marinades at room temperature keep meat in the danger zone. Refrigerator storage is still required.

One additional point on enzyme marinades: they work fast. Fish should be in an enzyme marinade for no more than 15-30 minutes before the texture degrades. Chicken can handle 1-2 hours, beef 3-4 hours. These are refrigerator marination times — shorter exposure than acid marinades, not license for room-temperature marinating.

Timing by Protein

Protein	Acid Marinade Time (Fridge)	Enzyme Marinade (Fridge)
Beef (steak)	2 hours to 2 days	1-4 hours
Pork	2 hours to 1 day	30 min to 2 hours
Chicken	2 hours to 2 days max	30 min to 2 hours
Fish	15-30 minutes	15-30 minutes
Shrimp	15-30 minutes	Not recommended

These are maximums for quality, not just safety. Acid marinades do useful work in the first few hours — much of the flavor absorption and surface protein modification happens early. Beyond a point, you’re just waiting.

What acids actually do to meat proteins

Acid marinades work through a mechanism that’s genuinely interesting. Muscle proteins (primarily myosin and actin) have an isoelectric point — a pH at which they carry no net charge. Below the isoelectric point (pH around 5.0-5.4 for muscle proteins), the proteins take on a positive charge and begin to repel each other, loosening the muscle structure and allowing it to hold more water.

This is why yogurt marinades (lactic acid, pH around 4.5) and citrus marinades produce juicier, more tender results — they’re pulling the meat’s protein structure toward this looser, water-retaining state.

At very low pH (heavy acid concentrations), the proteins start to denature — the surface appears cooked or firmer, which is the ceviche effect. For most marinating purposes, you want the middle range: loosened but not denatured.

None of these protein changes have anything to do with killing bacteria. The bacteria are largely separate from the meat’s structural proteins, living on surfaces and (in ground meat) distributed throughout. Acid kills bacteria through a different mechanism — cell membrane damage and protein disruption inside the bacterial cell — and requires much higher concentrations for much longer than a palatable marinade provides.

The rule is simple and has no exceptions: marinate in the refrigerator. For everything else — timing, acid chemistry, enzyme effects — there’s nuance. For the temperature question, there isn’t.

What This Means for You

Marinate in the refrigerator for 2 hours to overnight. Set aside a portion of fresh marinade before adding meat if you want it as a sauce. If you want to use the used marinade, boil it to 165°F first. Don't marinate chicken longer than 2 days. Bring meat briefly to refrigerator temperature before cooking — don't let it sit on the counter for 30+ minutes to 'take the chill off.'