There are many things that fall under that. Let me rattle of a few off the top of my head: (1) diet composition affects how eagerly your body stores energy in fat (related to sugars & insulin) - see eg https://www.physiology.org/doi/abs/10.1152/ajpendo.00283.201..., (2) different foods take varying amounts of energy to digest in the body (eg proteins and high fiber foods vs fast carbs), (3) the body's metabolic rate partly depends on how you eat and starts to conserve energy if you have long periods between meals, (4) your diet and rythm of meals also affects your general feeling of activity which can make you a couch potato or a evening walk person, (5) check out the research on intermittent fasting and ketogenic diets.

But this is not the main problem with the calories-in-calories-out meme; the main problem is that the feeling of hunger and appetite counts, not calories eaten. Satiety feelings are what regulates food intake in most people. Counting calories is not a solution to the obesity epidemic because continuously exerting willpower against your natural feeling of appetite is not sustainable for the vast majority of people.