Atheism will need to be combined with something else, something more constructive than its opposition to religion, to be relevant to our lives. The only possibility is to embrace morality as natural to our species.
— from The Bonobo and the Atheist (2013)
In 1975, De Waal began a six-year project on the world's largest captive colony of chimpanzees at the Arnhem Zoo. The study resulted in many scientific papers, and resulted in publication of his first book, Chimpanzee Politics, in 1982. This book offered the first description of primate behavior explicitly in terms of planned social strategies. De Waal was first to introduce the thinking of Machiavelli to primatology, leading to the label "Machiavellian Intelligence" that later became associated with it. In his writings, De Waal has never shied away from attributing emotions and intentions to his primates, and as such his work inspired the field of primate cognition that, three decades later, flourishes around themes of cooperation, altruism, and fairness.
His early work also drew attention to deception and conflict resolution, nowadays two major areas of research. Initially, all of this was highly controversial. Thus, the label of "reconciliation", which De Waal introduced for reunions after fights, was questioned at first, but is now fully accepted with respect to animal behavior. Recently, De Waal's work has emphasized non-human animal empathy and even the origins of morality. His most widely cited paper, written with his former student Stephanie Preston, concerns the evolutionary origin and neuroscience of empathy, not just in primates, but in mammals in general.
De Waal's name is also associated with bonobos, the "make love – not war" primates that he has made popular. But even his bonobo studies are secondary to the larger goal of understanding what binds primate societies together rather than how competition structures them.
Being both more systematically brutal than chimps and more empathic than bonobos, we are by far the most bipolar ape. Our societies are never completely peaceful, never completely competitive, never ruled by sheer selfishness, and never perfectly moral.
Competition is not ignored in his work: the original focus of de Waal's research, before he was well known, was aggressive behavior and social dominance. Whereas his science focuses on the behavior of nonhuman primates (mostly chimpanzees, bonobos, macaques, and capuchin monkeys), his popular books have given de Waal worldwide visibility by relating the insights he has gained from monkey and ape behavior to human society. With his students, he has also worked on elephants, which are increasingly featured in his writings.
His research into the innate capacity for empathy among primates has led De Waal to the conclusion that non-human great apes and humans are simply different types of apes, and that empathic and cooperative tendencies are continuous between these species. His belief is illustrated in the following quote from The Age of Empathy: "We start out postulating sharp boundaries, such as between humans and apes, or between apes and monkeys, but are in fact dealing with sand castles that lose much of their structure when the sea of knowledge washes over them. They turn into hills, leveled ever more, until we are back to where evolutionary theory always leads us: a gently sloping beach."
This is quite opposite to the view of some economists and anthropologists, who postulate the differences between humans and other animals. However, recent work on prosocial tendencies in apes and monkeys supports de Waal's position. See, for example, the research of Felix Warneken, a psychologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. In 2011, de Waal and his co-workers were the first to report that chimpanzees given a free choice between helping only themselves or helping themselves plus a partner, prefer the latter. In fact, de Waal does not believe these tendencies to be restricted to humans and apes, but views empathy and sympathy as universal mammalian characteristics, a view that over the past decade has gained support from studies on rodents and other mammals, such as dogs. He and his students have extensively worked on such cooperation and fairness in animals. In 2011 de Waal gave a TED Talk entitled "Moral behavior in animals". Part of the talk dealt with inequity aversion among capuchin monkeys, and a video extract of this went viral. It showed the furious reaction of one monkey given a less desirable treat than another. The most recent work in this area was the first demonstration that given a chance to play the Ultimatum game, chimpanzees respond in the same way as children and human adults by preferring the equitable outcome.
His 2013 book The Bonobo and the Atheist examines human behavior through the eyes of a primatologist, and explores to what extent God and religion are needed for human morality. The main conclusion is that morality comes from within, and is part of human nature. The role of religion is secondary.
De Waal also writes a column for Psychologie Magazine, a popular Dutch monthly.
Since September 1, 2013, de Waal has been a distinguished professor (universiteitshoogleraar) at Utrecht University. This is a part-time appointment—he remains in his position at Emory University, in Atlanta.
In June 2018, de Waal was awarded the NAT Award, recently established by the Museum of Natural Sciences of Barcelona. The award, which goes to people or institutions "that are referents for their way of viewing and explaining nature, whether because they have encouraged professional engagement in natural history disciplines or because they have contributed significantly to nature conservation", was awarded to de Waal "for his vision regarding the evolution of animal behaviour in establishing a parallel between primate and human behaviour in aspects such as politics, empathy, morality and justice." Alongside de Waal, broadcaster and naturalist David Attenborough was awarded an Extraordinary Award for a Professional Career, and biologist and former director of the Barcelona Zoology Museum Roser Nos Ronchera was awarded a Honorable Mention.