Internet-based cognitive behavior therapy (ICBT) has shown promising results in relation to treating many psychiatric disorders. However, research on the potential for negative effects of their use has been lacking. An individual patient data meta-analysis of 29 clinical trials of ICBT (N = 2866) was thus performed using the Reliable Change Index for each primary outcome measures to distinguish deterioration rates among patients in treatment and control conditions. Statistical analyses of predictors were conducted using generalized linear mixed models and binomial logistic regression. Missing data was handled by multiple imputation. Deterioration rates were 122 (5.8%) in treatment and 130 (17.4%) in control conditions. Relative to receiving treatment, patients in a control condition had higher odds of deteriorating, Odds Ratios (OR) 3.10, 95% Confidence Interval (CI) [2.21, 4.34]. Clinical severity at pre treatment was related to lower odds, OR 0.62, 95% CI [0.50, 0.77], and 0.51, 95% CI [0.51, 0.80], for treatment and control conditions. In terms of sociodemographic variables, being in a relationship, 0.58, 95% CI [0.35, 0.95], having at least a university degree, 0.54, 95% CI [0.33, 0.88], and being older, 0.78, 95% CI, [0.62, 0.98], were also associated with lower odds of deterioration, but only for patients in a treatment condition. In sum, deterioration among patients receiving ICBT or being in a control condition can occur and should be monitored by researchers in order to reverse and prevent a negative treatment trend.