Background Emotional disorders (EDs) are among the most prevalent mental disorders. Existing evidence-based psychological treatments are not sufficient to reduce the disease burden of mental disorders. It is therefore essential to implement innovative solutions to achieve a successful dissemination of psychological treatment protocols, and in this regard, the use of information and communication technologies such as the internet can be very useful. Furthermore, the literature suggests that not everyone with an ED receives the appropriate treatment. This situation has led to the development of new intervention proposals based on the transdiagnostic perspective, which attempts to address the underlying processes common to EDs. Most of these transdiagnostic interventions focus primarily on downregulating negative affectivity (NA), and less attention has been paid to strengths and the upregulation of positive affectivity, despite its importance for well-being and mental health. Objective This study aims to evaluate the efficacy of a transdiagnostic internet-based treatment for EDs in a community sample. Methods A 3-armed randomized controlled trial was conducted. A total of 216 participants were randomly assigned to a transdiagnostic internet-based protocol (TIBP), a TIBP+ positive affect (PA) component, or a waiting list (WL) control group. The treatment protocol contained core components mainly addressed to downregulate NA (ie, present-focused emotional awareness and acceptance, cognitive flexibility, behavioral and emotional avoidance patterns, and interoceptive and situational exposure) as well as a PA regulation component to promote psychological strengths and enhance well-being. Data on depression, anxiety, quality of life, neuroticism and extraversion, and PA/NA before and after treatment were analyzed. Expectations and opinions of treatment were also analyzed. Results Within-group comparisons indicated significant pre-post reductions in the two experimental conditions. In the TIBP+PA condition, the effect sizes were large for all primary outcomes (d=1.42, Beck Depression Inventory [BDI-II]; d=0.91, Beck Anxiety Inventory [BAI]; d=1.27, Positive and Negative Affect Schedule-Positive [PANAS-P]; d=1.26, Positive and Negative Affect Schedule-Negative [PANAS-N]), whereas the TIBP condition yielded large effect sizes for BDI-II (d=1.19) and PANAS-N (d=1.28) and medium effect sizes for BAI (d=0.63) and PANAS-P (d=0.69). Between-group comparisons revealed that participants who received one of the two active treatments scored better at posttreatment than WL participants. Although there were no statistically significant differences between the two intervention groups on the PA measure, effect sizes were consistently larger in the TIBP+PA condition than in the standard transdiagnostic protocol. Conclusions Overall, the findings indicate that EDs can be effectively treated with a transdiagnostic intervention via the internet, as significant improvements in depression, anxiety, and quality of life measures were observed. Regarding PA measures, promising effects were found, but more research is needed to study the role of PA as a therapeutic component. Trial Registration ClinicalTrials.gov NCT02578758; https://clinicaltrials.gov/ct2/show/NCT02578758 International Registered Report Identifier (IRRID) RR2-10.1186/s12888-017-1297-z