Food systems have changed markedly with human settlement and agriculture, industrialisation, trade, migration and now the digital age. Throughout these transitions, there has been a progressive population explosion and net ecosystem loss and degradation. Climate change now gathers pace, exacerbated by ecological dysfunction. Our health status has been challenged by a developing people-environment mismatch. We have regarded ecological conquest and innovative technology as solutions, but have not understood how ecologically dependent and integrated we are. We are ecological creatures interfaced by our sensoriness, microbiomes, shared regulatory (endocrine) mechanisms, immune system, biorhythms and nutritional pathways. Many of us are 'nature-deprived'. We now suffer what might be termed ecological health disorders (EHD). If there were less of us, nature's resilience might cope, but more than 9 billion people by 2050 is probably an intolerable demand on the planet. Future food must increasingly take into account the pressures on ecosystem-dependent food systems, with foods probably less biodiverse, although eating in this way allows optimal health; energy dysequilibrium with less physical activity and foods inappropriately energy dense; and less socially-conducive food habits. 'Personalised Nutrition', with extensive and resource-demanding nutrigenomic, metabolomic and microbiomic data may provide partial health solutions in clinical settings, but not be justified for ethical, risk management or sustainability reasons in public health. The globally prevalent multidimensional malnutritional problems of food insecurity, quality and equity require local, regional and global action to prevent further ecosystem degradation as well as to educate, provide sustainable livelihoods and encourage respectful social discourse and practice about the role of food.