Background: Protected Mealtimes is an intervention developed to address the problem of malnutrition in hospitalised patients through increasing positive interruptions (such as feeding assistance) whilst minimising unnecessary interruptions (including ward rounds and diagnostic procedures) during mealtimes. This clinical trial aimed to measure the effect of implementing Protected Mealtimes on the energy and protein intake of patients admitted to the subacute setting. Methods: A prospective, stepped wedge cluster randomised controlled trial was undertaken across three hospital sites at one health network in Melbourne, Australia. All patients, except those receiving end-of-life care or not receiving oral nutrition, admitted to these wards during the study period participated. The intervention was guided by the British Hospital Caterers Association reference policy on Protected Mealtimes and by principles of implementation science. Primary outcome measures were daily energy and protein intake. The study was powered to determine whether the intervention closed the daily energy deficit between estimated intake and energy requirements measured as 1900 kJ/day in the pilot study for this trial. Results: There were 149 unique participants, including 38 who crossed over from the control to intervention period as the Protected Mealtimes intervention was implemented. In total, 416 observations of 24-hour food intake were obtained. Energy intake was not significantly different between the intervention ([mean ± SD] 6479 ± 2486 kJ/day) and control (6532 ± 2328 kJ/day) conditions (p = 0.88). Daily protein intake was also not significantly different between the intervention (68.6 ± 26.0 g/day) and control (67.0 ± 25.2 g/day) conditions (p = 0.86). The differences between estimated energy/protein requirements and estimated energy/protein intakes were also limited between groups. The adjusted analysis yielded significant findings for energy deficit: (coefficient [robust 95% CI], p value) of -1405 (-2354 to -457), p = 0.004. Variability in implementation across aspects of Protected Mealtimes policy components was noted. Conclusions: The findings of this trial mirror the findings of other observational studies of Protected Mealtimes implementation where nutritional intakes were observed. Very few positive improvements to nutritional intake have been identified as a result of Protected Mealtimes implementation. Instead of this intervention, approaches with a greater level of evidence for improving nutritional outcomes, such as mealtime assistance, other food-based approaches and the use of oral nutrition support products to supplement oral diet, should be considered in the quest to reduce hospital malnutrition. Trial registration: Australian New Zealand Clinical Trials Registry: ACTRN12614001316695 ; registered 16th December 2014.