So what if the accused pleads NOT guilty?

As part of criminal procedure, the information (the criminal complaint that ripens into a criminal action in court) is read to the accused so that, in the most basic sense, s/he may be informed of the accusations against her/him. After that, the accused will be asked to enter a plea, i.e., s/he will tell the court if s/he will enter a plea of "guilty" or "not guilty."

["Plea" is a technical term in criminal procedure, which refers to a formal statement by or on behalf of a defendant or prisoner, stating guilt or innocence in response to a charge, offering an allegation of fact, or claiming that a point of law should apply.]

The accused must be arraigned before the court where the complaint or information was filed or assigned for trial. The arraignment shall be made in open court by the judge or clerk by furnishing the accused with a copy of the complaint or information, reading the same in the language or dialect known to him, and asking him whether he pleads guilty or not guilty. The prosecution may call at the trial witnesses other than those named in the complaint or information. (Section 1, Rule 116, Rules of Court)

When the accused enters a plea of guilt, the proceedings are shortened. In a nutshell, the accused admits the allegations by the prosecution and accepts that punishment will later be handed down against her/him. On the other hand, when the accused enters a plea of no guilt, the trial proceeds as usual.

After a "not guilty" plea is entered, the accused shall have at least fifteen (15) days to prepare for trial. The trial shall commence within thirty (30) days from receipt of the pre-trial order. (Section 1, Rule 119)

When we say the trial proceeds "as usual," we mean that the order of trial remains the same and the burden of proof is not affected. Under Section 11 of Rule 119 (Rules of Court), the trial for a criminal case shall proceed in the following order:
  1. The prosecution shall present evidence to prove the charge and, in the proper case, the civil liability.
  2. The accused may present evidence to prove his defense, and damages, if any, arising from the issuance of a provisional remedy in the case.
  3. The prosecution and the defense may, in that order, present rebuttal and sur-rebuttal evidence unless the court, in furtherance of justice, permits them to present additional evidence bearing upon the main issue.
  4. Upon admission of the evidence of the parties, the case shall be deemed submitted for decision unless the court directs them to argue orally or to submit written memoranda.
  5. When the accused admits the act or omission charged in the complaint or information but interposes a lawful defense, the order of trial may be modified.
Therefore, if the accused pleads not guilty, the prosecution still, as a rule, needs to present proof beyond reasonable doubt in order to secure conviction. Also, the burden of proof remains in the prosecution to prove that a crime has been committed and it was the accused who perpetrated it.

An accused has in his favor the presumption of innocence which the Bill of Rights guarantees. Unless his guilt is shown beyond reasonable doubt, he must be acquitted. This reasonable doubt standard is demanded by the due process clause of the Constitution which protects the accused from conviction except upon proof beyond reasonable doubt of every fact necessary to constitute the crime with which he is charged. The burden of proof is on the prosecution, and unless it discharges that burden the accused need not even offer evidence in his behalf, and he would be entitled to an acquittal. Proof beyond reasonable doubt does not, of course, mean such degree of proof as, excluding the possibility of error, produce absolute certainty. Moral certainty only is required, or that degree of proof which produces conviction in an unprejudiced mind. The conscience must be satisfied that the accused is responsible for the offense charged. (G.R. No. 205745, March 8, 2017)

The case is not lost simply because the accused pleads not guilty. However, if s/he did commit the crime and this is provable in court, s/he would be in a better position to simply enter a guilty plea in order to ensure that her/his days in jail would be shorter.