The present study assessed the changes in faecal microbial activity in obese Wistar rats fed high-fat or low-fat diets supplemented with various forms of chromium (picolinate or nanoparticles). The 18-week study was divided into two phases: an introductory period (9 weeks; obesity status induction via a high-fat diet) and an experimental period (9 weeks; maintained on a high-fat diet or switched to a low-fat diet and Cr supplementation). During the experimental period (10–18 weeks of feeding), samples of fresh faeces were collected on chosen days. The bacterial enzymatic activity and short-chain fatty acids (SCFAs) concentration were assessed to characterise the dynamism of the changes in faecal microbial metabolic activity under the applied dietary treatments. The results indicated that faecal microbial metabolic activity displayed several adaptation mechanisms in response to modifications in dietary conditions, and a beneficial outcome resulted from a pro-healthy dietary habit change, that is, switching from a high-fat to a low-fat diet. Dietary supplementation with chromium nanoparticles further modulated the aforementioned microbial activity, i.e., diminished the extracellular and total enzymatic activities, while the effect of chromium picolinate addition was negligible. Both the high-fat diet and the addition of chromium nanoparticles reduced SCFA concentrations and increased the faecal pH values.