Cleaner Protein for Stronger Performance: Why Athletes Should Rethink Their Fuel

A study finds diets high in processed foods increase stress on muscles and knees. Here are expert tips on better protein sources for athletes.

Athletes put in the work at the gym, on the track, at practice, and on the trails with the goal of becoming stronger, faster, and more powerful in their sport. However, all athletes know that progress isn’t possible without also focusing on their diet. What we eat is just as important as the miles run, weights lifted, or number of drills completed. Protein is one of the most important components of an athlete’s diet because it supports muscle growth and repair while also providing lasting energy.

It’s great that runners, volleyball players, basketball stars, and gym-goers are paying attention to the importance of protein, but athletes should focus more on cleaner protein sources. It’s quick and convenient to reach for options like powders, bars, shakes, and gels. However, these options may not be supporting performance in the way athletes think if they are packed with ultra-processed ingredients.

It’s true that mindful athletes are often choosing products made with more natural ingredients when it comes to sports nutrition. However, many growing teenage athletes are still stopping at fast-food restaurants after practice, snacking on junk food at school and home, or indulging in processed foods like hot dogs more often during the warmer months. Consuming a diet high in processed foods can sneak up on an athlete and actually hurt their muscles if they are not careful.

According to a new study published in the journal Radiology, researchers found that diets high in ultra-processed foods are linked to fat infiltration within thigh muscles, weakening muscle quality, increasing stress on the knees, and raising the risk of long-term joint issues.

The researchers used MRI scans from a knee osteoarthritis study and, in one case, found that a participant with a diet high in processed foods had muscles that appeared marbled, similar to Wagyu steak. And athletes should prevent this if they want to remain healthy.

Why Rethink How You Refuel

Athletes should rethink their diets and how they refuel after exercise to avoid consuming too many processed foods.

Better Recovery

“Cleaner” foods—whole foods without artificial ingredients and additives—rich in protein, healthy fats, vitamins, and carbohydrates help repair muscles faster and reduce soreness after practices, races, and matches more efficiently than foods packed with fillers, additives, and preservatives.

More Consistent Energy

Highly processed foods and sugary snacks provide a quick burst of energy, but they often lead to crashes later. Cleaner snacks and meals made with whole foods provide steady energy that helps athletes stay focused and strong throughout the day.

Improved Performance

When athletes eat well, they give their bodies the nutritional support needed to perform at their best. Eating a balanced diet helps support muscle growth and endurance, powers speed, improves hydration, and boosts mental focus. Gaps in an athlete’s diet can negatively affect all of these areas.

Reduced Inflammation

Many whole foods—such as fruits, vegetables, lean proteins, nuts, and healthy fats—contain nutrients that help fight inflammation. This aids in muscle recovery and lowers the risk of injury.

What “Cleaner” Eating Means

Cleaner eating doesn’t mean being perfect or restrictive. It usually means focusing more on:

• Lean proteins
• Fruits and vegetables
• Whole grains
• Healthy fats
• Plenty of water

And limiting:

• Excess added sugars
• Highly processed snacks
• Artificial ingredients
• Fast food

Athletes should also consider cleaner protein sources to support muscle recovery without unnecessary additives.

Expert Tips for Cleaning Up Protein Sources

1. Rethink Convenience, Don’t Eliminate It

Athletes are busy balancing school and sports. Runners spend all day at track meets, while volleyball players may compete in tournaments that last into the afternoon. Convenience matters, especially during training and race days.

According to Kimberlie Le, founder of Prime Roots, a food company creating fungi-based deli meats as a less processed alternative to traditional cold cuts, it’s okay to grab quick snacks—as long as they contain better ingredients.

“The goal isn’t to cut out quick protein sources, but to choose options that are less processed and made with simpler ingredients whenever possible,” she said.

2. Build Meals Around More Balanced Protein Sources

Meals that support recovery are essential for athletes.

“For recovery, prioritize meals that include protein from whole or minimally processed sources like eggs, chicken, fish, beans, lentils, yogurt, nuts, or fungi-based proteins,” Le said. “These types of proteins are often easier to digest and more bioavailable than highly processed powders and isolates, while also providing more sustained energy and support for long-term muscle maintenance and recovery.”

3. Upgrade Your Go-To Sandwich

Sandwiches are one of the most common and convenient meals for student-athletes. Small swaps can help clean up a diet.

“Swapping traditional deli meats for a cleaner option, like fungi-based deli meats from Prime Roots, can be an easy way to reduce overall intake of additives while still getting protein in a familiar, satisfying format,” Le said.

4. Pay Attention to Ingredient Lists, Not Just Protein Grams

“Many protein bars and shakes are marketed around high protein content, but it’s important to look beyond the label,” Le said. “Shorter ingredient lists and recognizable ingredients are a good sign you’re choosing a cleaner option.”

5. Balance Quick Fuel With Long-Term Performance

There is still a small place for processed sports nutrition products when needed.

“But relying on them as a primary protein source over time may not support muscle quality, digestion, and recovery as well as more balanced, whole-food-based options,” Le explained.

6. Focus on Consistency, Not Perfection

“You don’t have to overhaul your entire routine,” Le added. “Even small swaps, like upgrading one meal or snack per day, can make a meaningful difference in how you fuel and recover.”